From: Evandro Semighini (epsemighini_at_gmail.com)
Date: Tue Apr 14 2015 - 15:51:17 CDT
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
2015-04-14 17:45 GMT-03:00 Bennion, Brian <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 [owner-namd-l_at_ks.uiuc.edu] on behalf of
> Evandro Semighini [epsemighini_at_gmail.com]
> *Sent:* Tuesday, April 14, 2015 1:30 PM
> *To:* namd-l_at_ks.uiuc.edu
> *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 ?
> Thank you,
> Evandro Semighini
> University of São Paulo - Brazil
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