Re: [AMBER] Trouble obtaining force field parameters via Antechamber

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Thu, 06 Mar 2014 07:50:12 +0100

Dear Hyun-seok Kim,

I used your input PDB file to generate a FF using R.E.D. Python at
R.E.D. Server Dev. http://q4md-forcefieldtools.org/REDS-Development/
It took 5 sec to upload your PDB file; writing this email to report
the results was far longer ;-)

See
http://q4mdfft:q4mdfft2012.cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF2_Hyun-seok-Kim/P11471.html

your input molecule:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF2_Hyun-seok-Kim/P11471/Mol_red1.pdb

the FF lib with RESP charges and FF atom types:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF2_Hyun-seok-Kim/P11471/Data-R.E.D.Server/Mol_m1/Mol-sm_m1-c1.mol2

the FF parameters:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF2_Hyun-seok-Kim/P11471/Data-R.E.D.Server/Data-Default-Proj/frcmod.known
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF2_Hyun-seok-Kim/P11471/Data-R.E.D.Server/Data-Default-Proj/frcmod.unknown
(one missing FF param. easy to determine by analogy)

the leap script:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF2_Hyun-seok-Kim/P11471/Data-R.E.D.Server/Data-Default-Proj/leaprc.ff13q4mdfft

regards, Francois


> HI, I'm trying to obtain force field parameters via Antechamber.
>
> First, I've made a pdb file by myself from coordinate information(XYZs)
> using VMD.
>
> Then, I've converted to mol2 file and obtained 'frcmod' file via
> Antechamber.
>
> However, I get correct number of bonds but everything else is missing.
>
> I guess the pdb file I've made is causing the trouble.
>
> (sustiva.pdb from AMBER example works fine)
>
>
>
> Any suggestions to make a firm pdb file from coordinate information?
>
> I'm attaching the pdb file I've made.



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Received on Wed Mar 05 2014 - 23:00:03 PST