From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Fri Apr 24 2015 - 12:27:51 CDT
Hello Evandro,
Your description below is still missing critical information and blending steps together without any stated rationale.
At this point it would be best if you posted your initial molecule structure file so others could check it and reproduce your errors.
If this is not acceptable for whatever reason lets talk off-line.
Brian
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Evandro Semighini
Sent: Friday, April 24, 2015 8:05 AM
To: Mayne, Christopher G
Cc: <namd-l_at_ks.uiuc.edu>
Subject: Re: namd-l: Re: Problems to parametrize molecules
Hello Christopher,
I did what you said in the first message, with another molecule, and I got the message of "unknown residue" when I try to create the psf file with psfgen, even with the str file from ParamChem, as this unknown residue is the whole molecule.
I looked to it again and the residue name is the same at the pdb and the mol2 file, UNK.
I only managed to run psfgen dividing the molecule into parts like a benzene ring, a phenyl methyl ketone system and so on, taking it's parameters from the cgenff rtf file and modifying them, removing the atoms where is another part from the original molecule, but when I try to parametrize more than one part toghether in the same molecule, it only parametrizes the first part, as it recozniges it as the only residue there, and the bonds are completelly messed.
So, I changed the rtf file to this (benzene):
RESI BENZ 0.00 ! C6H6 benzene, adm jr.
GROUP
ATOM CG CG2R61 -0.115
ATOM CZ CG2R61 0.000 ! HD1 HE1
ATOM CD1 CG2R61 -0.115 ! | |
ATOM HD1 HGR61 0.115 ! CD1--CE1
ATOM CD2 CG2R61 -0.115 ! / \
ATOM HD2 HGR61 0.115 ! *-CG CZ-*
ATOM CE1 CG2R61 -0.115 ! \ /
ATOM HE1 HGR61 0.115 ! CD2--CE2
ATOM CE2 CG2R61 -0.115 ! | |
ATOM HE2 HGR61 0.115 ! HD2 HE2
BOND CD1 CG CD2 CG CE1 CD1
BOND CE2 CD2 CZ CE1 CZ CE2
BOND CD1 HD1 CD2 HD2 CE1 HE1
BOND CE2 HE2
IC CG CD1 CE1 CZ 0.0000 0.0000 0.0000 0.0000 0.0000
IC CD1 CE1 CZ CE2 0.0000 0.0000 0.0000 0.0000 0.0000
IC CE1 CZ CE2 CD2 0.0000 0.0000 0.0000 0.0000 0.0000
IC CE1 CG *CD1 HD1 0.0000 0.0000 180.0000 0.0000 0.0000
IC CE2 CG *CD2 HD2 0.0000 0.0000 180.0000 0.0000 0.0000
IC CZ CD1 *CE1 HE1 0.0000 0.0000 180.0000 0.0000 0.0000
IC CZ CD2 *CE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000
psfgen runned, resulting in 64 atoms, but, it has a lot of errors like this:
psfgen) ERROR: Missing atoms for bond CE2(0) HE2\PAR(0) in residue BENZ:2
psfgen) Warning: failed to set coordinate for atom C10 BENZ:2
psfgen) no segment
All over the molecule, and all the bonds are still wrong.
I checked the str, pdb and mol2 files, they are ok.
Any clue of where I am missing this process ?
I will have to do this customized parameters for every molecule I'm working with ?
Thank you,
Evandro
2015-04-19 20:59 GMT-03:00 Mayne, Christopher G <cmayne2_at_illinois.edu<mailto:cmayne2_at_illinois.edu>>:
Evandro,
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.
Regards,
Christopher Mayne
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