Comments (3)
Sorry, the answer is very clear, you gave a PDB with many residues, it won't work, you need a pdb with only one residue, the one you want the topology. Read here for an example. Though it's not updated yet, it shows what you have to do.
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Thanks for the observations. This tutorial still need to be updated. I probably used gmx_d
for double precision or multi-cpus, I don't remember the detail anymore. I'll try to do a first round of update asap.
I do intend to add more tutorial and certainly I intend to address protein-ligand interactions energy but I don't know when I'll find time.
Also, I do like Justin's tutorials because they are really rich in details. Don't get me wrong but we try to put in few pages many years of experience and, though it may look "simpler" now, the devil's always in the details.
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Related Issues (20)
- How much time is expected to complete an instalation using conda? HOT 7
- Conda installs "full" ambertools, no writing of CHARMM ff files HOT 2
- Error while generating topologies HOT 3
- No Charge value given and wrong assigned bond types HOT 1
- Re-running ACPYPE with same molecule with different formal charges doesn't update the GMX itp HOT 1
- more water models from Amber HOT 2
- multiple chain protein HOT 3
- wrong converted charge HOT 3
- Planarity of the benzene ring not maintained in dynamics. HOT 8
- acpype error HOT 1
- charmm input format HOT 1
- '1-4 pairs were missing' warning when parsing the converted topology with ParmED HOT 4
- is this a bug? HOT 3
- atom type does not exist in parmchk.dat HOT 3
- Is there a way to control the threads? HOT 3
- Is the GMX_OPLS still experimental? HOT 3
- A question about the content of md.mdp file HOT 1
- [question] does it automatically protonates molecules for a given pH? HOT 1
- [question] what are the partial charges being used? HOT 1
- conversion of Amber files to gromacs HOT 3
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