Re: Re: Problems to parametrize molecules

From: Mayne, Christopher G (
Date: Sun Apr 19 2015 - 18:59:20 CDT


Small molecules are typically treated as single residues; certainly anything returned by ParamChem is treated as a single residue. It is critical that the information in your PDB, i.e., resname, atom names, etc., matches that of your MOL2 file, since this is what ParamChem uses to build the topology. You should specifically check the resname, as ParamChem may assign UNK if the resname in the MOL2 isn't assigned or valid.

Christopher Mayne

On Apr 19, 2015, at 6:47 PM, Evandro Semighini wrote:

Hello Christopher,

Thank you !

Problem #1

Yes, I always uploaded mol2 files, I tried even to upload them converted from diferent softwares to check if that was the problem, but it wasn't.
I am using VMD 1.9.2, as I began with NAMD this month. I prepare the files at windows and send them to a linux server to run the simulations.

Thank you for the pgn file.

I did as you said and things gone the same way, it doesn't recognize the UNK residue (that come like this as an output from the docking software).
So, I edited the molecule to put the residues, like is in the cgenff file (a benzene ring, BENZ and so on), and psfgen finally runned with my molecule--_000_C68FF29BD15F43368CDD2C035859C40Dillinoisedu_--

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