choderalab/ambermini

A stripped-down set of just antechamber, sqm, and tleap.

ambermini's Issues

Windows uses?

I was wondering what the use-case is here for supporting Windows? Is anybody actively using WIndows versions of ambermini?

AmberTools17 update

Hey guys,

Are you planning on updating to AmberTools17? Do you need any help?

Best,
João

Compiling problems of arpack with gfortran-10

I was trying to compile ambermini on the new debian with gfortran-10. And I got this error during the compilation stage:

gfortran -c -O3   -I/home/ludwig/git/ambermini/include    -Wall -o dgetv0.o dgetv0.f
dgetv0.f:403:32:

  367 |           call dvout (logfil, 1, rnorm0, ndigit,
      |                                 2
......
  403 |          call dvout (logfil, n, resid, ndigit,
      |                                1
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (scalar and rank-1)
make: *** [Makefile:7: dgetv0.o] Error 1

An ideas of how to address this?
Thank you

Conda packaging trial

I've created a test conda package and uploaded it to binstar.

Give this a try (assuming you have already installed and initialized conda):

conda config --add channels https://conda.binstar.org/jchodera
conda install ambermini
# if using tcsh, may need to "rehash" file paths
antechamber -L

The one drawback is that all of the tools in the repo seem to return exit code 1 when called with arguments asking for help, meaning that it's not possible for the conda build ambermini I used to build the conda package to test them successfully. This would probably require adding a tiny test/ directory to ambermini with one example that could actually be run by antechamber and tleap.

The packaging scripts are in a PR here:
https://github.com/rmcgibbo/conda-recipes/pull/2

Update for AmberTools 15?

@swails and @davidlmobley, we need to update this for AmberTools15.

What's the best way to proceed here?

Add reduce to ambermini?

It would be very useful to include reduce in ambermini.

Alternatively, I've seen one anaconda cloud channel make reduce available separately, and we could add a recipe to build it as a standalone tool in omnia.

Update conda recipe md5 for 14.0.1 release

https://github.com/omnia-md/conda-recipes/blob/master/ambermini/meta.yaml

Update strategy to keep in sync with ambertools

We should adopt a strategy to keep this repo in sync with ambertools.

Xfer ownership?

@jchodera and @kyleabeauchamp: The target purpose of this package is essentially to service gaff2xml. Does it make sense to transfer this repo to @choderalab so that you guys don't have to rely on me to merge PRs and make changes? It'll also let you control the releases to meet your needs.

@jchodera made me a member of @choderalab, so I think you can set it up so I can continue to directly modify it...

OPC water and 12_6_4 parameters

I was trying to create system with OPC water and used 12_6_4 parameters for Mg2+. Is it possible? Unfortunately, i had an error, that said that i need to choose tip3p, spce or tip4p water. I had latest version (amber 20).

'sqm -h' fails

conda build ambermini now fails with

+ sqm -h

     Error unknown flag: -h                                                                              

which is odd, since this worked fine in AmberTools 14:

[LSKI1497:~] choderaj% sqm -h
sqm [-O] -i <input> -o <output>
   -O           Overwrite output file if it exists
   -i <input>   Input file
   -o <output>  Output file
   -h           Show this message

How to handle AmberMini Development going forward

#37 showed that the current way of managing AmberMini is not sustainable and we will need a new strategy.

Based on feedback from #37, it should be possible to compile the parts of AmberTools that we want, create wrappers for the executables we want, and ship that. However, the tests are less simple to bundle this way for the following reasons:

1. Inconsistent test structure, likely due to years of AmberTools dev and old tests never being updated.
2. Reliance on the $AMBERHOME variable to find file structure
3. Reliance on the config.h file created from the ./configure command at standard AmberTools install

I think we can use the above scheme and address the issues above with the following items (not 1-to-1 with above)

1. Create a compile script which builds only the parts we want and would be the major script updated for new versions of AmberMini
2. Create wrappers for the executables we need to have an OS agnostic platform which also handle at-run-time assignment of $AMBERHOME
3. Carry the config.h file from the compiled versions of AmberTools when updating AmberMini into the test directory and have all tests reference it.

This is not something that has to be fixed "right now" but it is something that should be addressed by AmberTools 17, or whatever the next major version is.

Other options are welcome (such as coordinating an official AmberLite)

Issues with osx ambermini package

I'm having trouble running the osx ambermini package:

Running: /Users/choderaj/projects/project-icarus/trypsin-benzamidine/setup/conda-env-trypsin-benzamidine/bin/../bin/sqm -O -i sqm.in -o sqm.out
dyld: Library not loaded: /usr/local/gfortran/lib/libquadmath.0.dylib
  Referenced from: /Users/choderaj/projects/project-icarus/trypsin-benzamidine/setup/conda-env-trypsin-benzamidine/bin/../bin/sqm
  Reason: image not found
Error: cannot run "/Users/choderaj/projects/project-icarus/trypsin-benzamidine/setup/conda-env-trypsin-benzamidine/bin/../bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit

How to change sqm.out directory when using antechamber to convert pdb to mol2?

Hi,

I want to use antechamber to convert pdb file to mol2 by this command:

antechamber -fi pdb -i $work_path/ligand3.pdb -fo mol2 -o $work_path/ligand4.mol2 -c bcc -pf y

I would like to place sqm.out in the same directory of mol2. In this case, it needs placing in $work_path directory.

I do not know how to do this. Please help me. Thank you very much.

Parmchk and AMBERHOME

Can you remind me about the status of wrapping parmchk to avoid the AMBERHOME dependency? I just tried building from source and John's binstar versions and I still am having issues:

kyleb@kb-intel:~/src/choderalab/gaff2xml/tmp$ parmchk -h
AMBERHOME is not set!
kyleb@kb-intel:~/src/choderalab/gaff2xml/tmp$ parmchk2 -h
AMBERHOME is not set!

YACC dependency

On a Linux system I'm using, I am apparently missing YACC:

+ ./configure --prefix=/cbio/jclab/share/anaconda/install/envs/_build
YACC cannot be found!

It's not easy to package up YACC too, I imagine? Or is this something expected on most Linux systems.

There doesn't seem to be a conda YACC package...

GLIBC Hell

So I'm finding that the 14.0.1 release of ambermini no longer works on our cluster due to the usual GLIBC nonsense:

-bash-4.1$ conda install -c https://conda.binstar.org/omnia ambermini
The following NEW packages will be INSTALLED:

    ambermini: 14.0.1-0
-bash-4.1$ parmchk2
/cbio/jclab/home/kyleb/opt/bin/parmchk2_pvt: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /cbio/jclab/home/kyleb/opt/bin/parmchk2_pvt)

However, I find that using an older version from @pgrinaway seems to work:

-bash-4.1$ ls /cbio/jclab/home/pgrinaway/anaconda/pkgs/ambermini*.bz2
/cbio/jclab/home/pgrinaway/anaconda/pkgs/ambermini-14.0.1-0.tar.bz2  /cbio/jclab/home/pgrinaway/anaconda/pkgs/ambermini-14-0.tar.bz2

conda install /cbio/jclab/home/pgrinaway/anaconda/pkgs/ambermini-14-0.tar.bz2

-bash-4.1$ parmchk2 
AMBERHOME is not set!
-bash-4.1$ antechamber
Usage: antechamber -i   input file name
                   -fi  input file format

I'm trying to figure out what has changed since the last build. I also tried rebuilding using my Centos6.5 virtual machine, to no avail.

(Also, I had to add sudo yum install gcc-gfortran to the VM to make it work, which we should add to the VM once we figure out how to get this working).

Ran into issue with binstar build

I'm testing out the use of binstar-build to build the openmoltools project.

I ran into a problem with their docker environment and the ambermini dependency where a library used to build sqm was not found:
https://anaconda.org/omnia/openmoltools-dev/builds/6/0#L841

Any ideas on a way around this?

pdb4amber?

Does pdb4amber get installed with ambermini? I don't see it getting put into the path.

Add gcc dependency to make building easier?

There is now a gcc conda package complete with fortran compiler that will make building simpler.

sqm regression from AmberTools14 to 15?

Feeding the same exact mol2 file to

antechamber -i bosutinib.mol2 -fi mol2 -o bosutinib.gaff.mol2 -fo mol2 -s 2 -c bcc -nc 1

gives me no problems with ambermini 14.0.1, and throws an error with ambermini 15.0.4. More specifically (from sqm.out)

QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after   1000 steps.
QMMM: E =  -0.1350E+07 DeltaE =   0.1081E+00 DeltaP =   0.3423E-01
QMMM: Smallest DeltaE =   0.2736E-03 DeltaP =   0.8028E-02 Step =     11

In case you'd like to reproduce it, this is the file mol2 file I'm using

@<TRIPOS>MOLECULE
4-(2,4-dichloro-5-methoxy-anilino)-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile
66   69    1
SMALL
USER_CHARGES


@<TRIPOS>ATOM
      1 C1          5.6596    2.1116    0.3482 C.ar      1 BOS        -0.1126 
      2 C2          4.2762    2.1505    0.4965 C.ar      1 BOS         0.0873 
      3 C3          3.5468    3.1512   -0.1335 C.ar      1 BOS         0.1223 
      4 C4          4.2021    4.1102   -0.9099 C.ar      1 BOS        -0.2145 
      5 C5          5.5843    4.0953   -1.0751 C.ar      1 BOS         0.4306 
      6 C6          6.3184    3.0763   -0.4327 C.ar      1 BOS        -0.1750 
      7 C7          7.7099    3.0608   -0.5989 C.ar      1 BOS         0.2632 
      8 C8          8.3307    4.0277   -1.3765 C.ar      1 BOS        -0.1715 
      9 C9          7.5291    4.9845   -1.9653 C.ar      1 BOS         0.4609 
     10 N1          6.1841    5.0350   -1.8303 N.ar      1 BOS        -0.6632 
     11 C10         9.7450    4.0615   -1.5824 C.1       1 BOS         0.2440 
     12 N2         10.8938    4.0889   -1.7497 N.1       1 BOS        -0.3588 
     13 N3          8.5017    2.0609    0.0227 N.pl3     1 BOS        -0.6909 
     14 C11         8.9227    0.7909   -0.3984 C.ar      1 BOS         0.1942 
     15 C12         9.7144   -0.0179    0.4170 C.ar      1 BOS        -0.0281 
     16 C13        10.1175   -1.2764   -0.0296 C.ar      1 BOS        -0.0841 
     17 C14         9.7291   -1.7260   -1.2916 C.ar      1 BOS        -0.0178 
     18 C15         8.9375   -0.9172   -2.1070 C.ar      1 BOS         0.1329 
     19 C16         8.5344    0.3413   -1.6604 C.ar      1 BOS        -0.1798 
     20 O1          8.5432   -1.3307   -3.3447 O.3       1 BOS        -0.3368 
     21 C17         7.3100   -2.0415   -3.4272 C.3       1 BOS         0.1152 
     22 Cl1        10.2412   -3.2866   -1.8188 Cl        1 BOS        -0.0645 
     23 Cl2        10.2169    0.5004    1.9867 Cl        1 BOS        -0.0752 
     24 O2          2.1845    3.2092   -0.0018 O.3       1 BOS        -0.3346 
     25 C18         1.4214    3.1112   -1.1971 C.3       1 BOS         0.1326 
     26 C19         0.0813    2.4629   -0.8715 C.3       1 BOS        -0.0884 
     27 C20         0.2286    1.0645   -0.2864 C.3       1 BOS         0.1804 
     28 N4          0.9127    0.1466   -1.1951 N.3       1 BOS        -0.7398 
     29 C21         0.0085   -0.3024   -2.2609 C.3       1 BOS         0.1725 
     30 C22         0.7238   -1.2674   -3.2127 C.3       1 BOS         0.1670 
     31 N5          1.2632   -2.4194   -2.4801 N.4       1 BOS        -0.7319 
     32 C23         2.1683   -1.9706   -1.4149 C.3       1 BOS         0.1670 
     33 C24         1.4542   -1.0049   -0.4630 C.3       1 BOS         0.1725 
     34 C25         1.9460   -3.3388   -3.3883 C.3       1 BOS         0.1576 
     35 O3          3.6529    1.2086    1.2565 O.3       1 BOS        -0.3318 
     36 C26         3.4864    1.4996    2.6432 C.3       1 BOS         0.1161 
     37 H1          6.2095    1.3189    0.8510 H         1 BOS         0.1529 
     38 H2          3.6134    4.8872   -1.3959 H         1 BOS         0.1656 
     39 H3          7.9448    5.7720   -2.5878 H         1 BOS         0.0373 
     40 H4          8.9067    2.2284    1.0316 H         1 BOS         0.4558 
     41 H5         10.7347   -1.9079    0.6061 H         1 BOS         0.1658 
     42 H6          7.9173    0.9682   -2.3003 H         1 BOS         0.1572
     43 H7          7.1132   -2.3139   -4.4746 H         1 BOS         0.0471 
     44 H8          6.4942   -1.4048   -3.0544 H         1 BOS         0.0471 
     45 H9          7.3713   -2.9542   -2.8162 H         1 BOS         0.0471 
     46 H10         1.2583    4.1170   -1.6115 H         1 BOS         0.0407 
     47 H11         1.9649    2.4965   -1.9298 H         1 BOS         0.0407 
     48 H12        -0.4554    3.0800   -0.1359 H         1 BOS         0.0654 
     49 H13        -0.5193    2.3813   -1.7895 H         1 BOS         0.0654 
     50 H14         0.8117    1.1163    0.6449 H         1 BOS         0.0320 
     51 H15        -0.7675    0.6496   -0.0727 H         1 BOS         0.0320 
     52 H16        -0.8548   -0.8189   -1.8159 H         1 BOS         0.0366 
     53 H17        -0.3412    0.5677   -2.8358 H         1 BOS         0.0366 
     54 H18         0.0128   -1.6303   -3.9695 H         1 BOS         0.0377 
     55 H19         1.5535   -0.7440   -3.7103 H         1 BOS         0.0377 
     56 H20         2.5178   -2.8408   -0.8399 H         1 BOS         0.0377 
     57 H21         3.0317   -1.4548   -1.8605 H         1 BOS         0.0377 
     58 H22         2.1742   -0.6543    0.2911 H         1 BOS         0.0366 
     59 H23         0.6334   -1.5415    0.0353 H         1 BOS         0.0366 
     60 H24         2.3409   -4.1922   -2.8176 H         1 BOS         0.0322 
     61 H25         2.7756   -2.8146   -3.8852 H         1 BOS         0.0322 
     62 H26         1.2353   -3.7014   -4.1456 H         1 BOS         0.0322 
     63 H27         2.9722    0.6605    3.1347 H         1 BOS         0.0458 
     64 H28         2.8862    2.4144    2.7564 H         1 BOS         0.0458 
     65 H29         4.4724    1.6482    3.1076 H         1 BOS         0.0458 
     66 H66         0.4254   -2.9639   -2.0201 H         1 BOS         0.0000 
@<TRIPOS>BOND
     1    1    6 ar   
     2    1    2 ar   
     3    1   37 1    
     4    2    3 ar   
     5    2   35 1    
     6    3    4 ar   
     7    3   24 1    
     8    4    5 ar   
     9    4   38 1    
    10    5   10 ar   
    11    5    6 ar   
    12    6    7 ar   
    13    7    8 ar   
    14    7   13 1    
    15    8    9 ar   
    16    8   11 1    
    17    9   10 ar   
    18    9   39 1    
    19   11   12 3    
    20   13   14 1    
    21   13   40 1    
    22   14   19 ar   
    23   14   15 ar   
    24   15   16 ar   
    25   15   23 1    
    26   16   17 ar   
    27   16   41 1    
    28   17   18 ar   
    29   17   22 1    
    30   18   19 ar   
    31   18   20 1    
    32   19   42 1    
    33   20   21 1    
    34   21   43 1    
    35   21   44 1    
    36   21   45 1    
    37   24   25 1    
    38   25   26 1    
    39   25   46 1    
    40   25   47 1    
    41   26   27 1    
    42   26   48 1    
    43   26   49 1    
    44   27   28 1    
    45   27   50 1    
    46   27   51 1    
    47   28   33 1    
    48   28   29 1    
    49   29   30 1    
    50   29   52 1    
    51   29   53 1    
    52   30   31 1    
    53   30   54 1    
    54   30   55 1    
    55   31   32 1    
    56   31   34 1    
    57   31   66 1    
    58   32   33 1    
    59   32   56 1    
    60   32   57 1    
    61   33   58 1    
    62   33   59 1    
    63   34   60 1    
    64   34   61 1    
    65   34   62 1    
    66   35   36 1    
    67   36   63 1    
    68   36   64 1    
    69   36   65 1    
@<TRIPOS>SUBSTRUCTURE
     1 BOS         1 GROUP             0       ****    0 ROOT

Set up appveyor

Now that we have windows support thanks to @rmcgibbo via #25

Conda package tests fails despite succeeding

See omnia-md/conda-recipes#249 (comment)

Incorrectly translated equation in gaff

Apologies if this has already been addressed, since the code is very old

In antechamber/charmmgen.c routine empangle, (https://github.com/choderalab/ambermini/blob/master/antechamber/charmmgen.c#L1120) there are the following lines of code:

dparm = (bondlength1 - bondlength2) * (bondlength1 - bondlength2);
dparm =
	dparm / (bondlength1 + bondlength2) * (bondlength1 + bondlength2);
force =
	143.9 * zparm1 * cparm * zparm2 * exp(-2 * dparm) / (bondlength1 + bondlength2);
force /= sqrt(angle * 3.1415926 / 180.0);

First concern: you will notice that the second line of code is probably not performing the calculation
intended by the original author.

Second concern: the last line is dividing by the square-root of the bend angle in radians. However, the
correct operation (Eq. 5 in Gaff paper, J Comput Chem 25: 1157–1174, 2004) would be to divide
by the square of the angle.

That said, employing the correct expressions results in values that don't appear correct. So perhaps
this same lines of code were used in the original fit for the Z and C parameters. In which case
correcting the code is not a good idea. But, perhaps a comment explaining the situation might
be helpful for the next person that encounters this.

bondtype and atomtype executables complain AMBERHOME is not set

While antechamber works just fine under conda, I just realized bondtype and atomtype want $AMBERHOME set.

Remove $AMBERHOME dependency for am1bcc?

Is it possible to remove the $AMBERHOME dependency for am1bcc?

[LSKI1497:ambermini/ambermini/bin] choderaj% ./am1bcc -h
AMBERHOME is not set!

Update to AmberTools 16

This is a discussion of what needs to be done to update ambermini to AmberTools 16

From @swails:

There was a massive reorganization of force fields that happened after I started my new job, and corresponding changes to tleap. The general goal of the FF work was to separate the protein and nucleic acid force fields into separate leaprc files, and files like leaprc.ff14SB were shuffled off into oldff.

I guess what needs to be done is to migrate the changes between AmberTools 15 and AmberTools 16 into ambermini (preferably without getting rid of the fixes for Windows and not having to set AMBERHOME). But that work was a large undertaking and was probably the main reason the release was delayed longer than expected.

Pinging @rafwiewiora who may want to know about this update since it impacts the forcefield conversion.

Conda recipe tests fails despite succeeding

See omnia-md/conda-recipes#249 (comment)

Compile error on OS X 10.9 with macports gcc 4.5.4

I've run into this:

NOTE: skipping the building of xleap as X11 libraries are not installed or
NOTE: -nox11 was specified as an option to configure.
/Applications/Xcode.app/Contents/Developer/usr/bin/make sqm
cd sqm && /Applications/Xcode.app/Contents/Developer/usr/bin/make install
gfortran -DBINTRAJ -DEMIL    -c -O0 -ffree-form  -I/Users/choderaj/code/yank/ambermini/ambermini.swails/include     -o file_io_dat.o file_io_dat.F90
make[2]: *** No rule to make target `../include/dprec.fh', needed by `constants.o'.  Stop.
make[1]: *** [sqm] Error 2
make: *** [all] Error 2

Set up travis-ci to build ambermini-dev conda package

This should follow the lead @rmcgibbo started with mdtraj

ambermini conda package still failing

I'm still seeing a failure from the tests:
https://jenkins.choderalab.org/job/conda-omnia-release-osx-2/148/console

It gets as far as tleap -h now, so I'm guessing that this is returning a nonzero integer:
https://github.com/omnia-md/conda-recipes/blob/master/ambermini/meta.yaml#L20-L23

Library dependency

I get the following error when I try to run tleap:

tleap -h
dyld: Library not loaded: /opt/local/lib/libgcc/libgcc_s.1.dylib
Referenced from: /Users/chayastern/anaconda/bin/teLeap
Reason: image not found
/Users/chayastern/anaconda/bin/tleap: line 19:   458 Trace/BPT trap: 5       $AMBERHOME/teLeap -I$AMBERHOME/../dat/leap/prep -I$AMBERHOME/../dat/leap/lib -I$AMBERHOME/../dat/leap/parm -I$AMBERHOME/../dat/leap/cmd $