From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Tue Apr 14 2015 - 15:57:28 CDT
still guessing but the psf file is not correct and that is what counts. I am not sure how you got your psf file from the pdb or mol2 but molefacture might be a plugin to use just to see the difference in the psf file that it creates compared to the current psf file.
From: Evandro Semighini [epsemighini_at_gmail.com]
Sent: Tuesday, April 14, 2015 1:51 PM
To: namd-l_at_ks.uiuc.edu; Bennion, Brian
Subject: Re: namd-l: Problems to parametrize molecules
Thank you Brian,
I thought that this as the problem too, but I don't know how to fix it, since the input files (pdb or mol2) have the correct bond orders.
I can change this with molefracture, before try the psfgen or the sites I tried ?
2015-04-14 17:45 GMT-03:00 Bennion, Brian <bennion1_at_llnl.gov<mailto:bennion1_at_llnl.gov>>:
I am just guessing here...
You need to pay attention to the what the error states. The errors suggest that the same atom is bonded to itself and it obviously cant find that in the parameter file.
From: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> [owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>] on behalf of Evandro Semighini [epsemighini_at_gmail.com<mailto:epsemighini_at_gmail.com>]
Sent: Tuesday, April 14, 2015 1:30 PM
Subject: namd-l: Problems to parametrize molecules
Hello NAMD community
I am trying to run NAMD with the results of virtual screening assays I made, but I am not being able to parametrize the molecules properly.
I read everything I found about it but, unfortunately, it didn't worked.
I tried charmmgui and paramchem webservers to generate the psf files, but when I try to run NAMD, theres always some unknown atom type (this errors are from two different molecules)
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG301 CG301 (ATOMS 22 22)
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR NG2S1 NG2S1 (ATOMS 8 8)
This atom types are at the par_all36_cgenff.prm and I added all the parameter files from the package to run this simulations.
There were no high penalties for the atoms from the servers.
Can you please help me to find where I am missing or show me where I should go to parametrize this molecules for the simulations ?
University of São Paulo - Brazil
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