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alanwilter / acpype

OFFICIAL: AnteChamber PYthon Parser interfacE
https://alanwilter.github.io/acpype/
GNU General Public License v3.0
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Acpype -I gives error `ACPYPE FAILED: Only ONE Residue is allowed for ACPYPE to work` #65

Closed gundalav closed 2 years ago

gundalav commented 2 years ago

I have the was trying a ligand pub file with acpype It's downloadable here.

But I get the following error

 $ acpype -i my_ligand.pdb
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2021.12.14 (c) 2021 AWSdS |
============================================================================
ERROR: more than one residue detected '{'PRO', 'GLN', 'LYS', 'TYR', 'THR', 'HIS', 'GLU', 'ASN', 'SER', 'CYS', 'ASP', 'GLY', 'PHE', 'MET', 'VAL', 'ALA', 'ARG'}'
ERROR: verify your input file 'my_ligand.pdb'. Aborting ...
ACPYPE FAILED: Only ONE Residue is allowed for ACPYPE to work
Total time of execution: less than a second

How can I resolve it?

-GV

alanwilter commented 2 years ago

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.

gundalav commented 2 years ago

Hi,

I found your website Tutorial Using ACPYPE for GROMACS https://github.com/alanwilter/acpype/wiki/Tutorial-Using-ACPYPE-for-GROMACS extremely useful. Much more straightforward than the GROMACS tutorial.

Would you please kindly add how to calculate the interaction energy following GROMACS initial tutorial here http://www.mdtutorials.com/gmx/complex/09_analysis.html?

We'd like to get interaction_energy.xvg file for final plotting.

Lastly, in your Run minimization and short simulation step you use gmx_d. Should it be gmx instead?

Sincerely, G.V.

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Closed #65 https://github.com/alanwilter/acpype/issues/65.

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alanwilter commented 2 years ago

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.