Re: [AMBER] generate frcmod.user file for missing parameters

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From: FyD <fyd.q4md-forcefieldtools.org>
Date: Fri, 11 Mar 2016 13:48:00 +0100

Jesmita Dhar,

> I have run the red server and I get the
> output. But when I have run the leaprc file to genetrate the topology
> file, a list of errors has been generated. I have to create an
> another frcmod,molecule (frcmod.user) file for the missing parameters.
> But I am unable to create the frcmod file by own. I will be greatfull
> if you please guide me how can I genarate the frcmod.user file.

when running a R.E.D. Server Dev./PyRED job first check the optimized
geometry:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFmyR4WopAADFKhpZR2zZdRFJrMFJ2zyAWADF/P1314/javaappletpdb-1.html
which loads Mol_m1/Mol_m1-c1-qmra.pdb

if correct (in your case I think your input molecule lack hydrogen
atoms) look at the atom types generated:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFmyR4WopAADFKhpZR2zZdRFJrMFJ2zyAWADF/P1314/javaappletmol2-1.html
which loads Mol_m1/Mol-sm_m1-c1.mol

if you agree with what is provided, yes, you can work on providing
unknown FF parameters listed in the frcmod.unknown file. if not
restart all over from the beginning with a correct PDB input file.

I CC this email to contact_at_q4md-forcefieldtools.org

regards, Francois

F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/

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Received on Fri Mar 11 2016 - 05:00:10 PST