AMBER Archive (2008)

Subject: Re: AMBER: using amber ports in Gromacs

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun May 25 2008 - 14:32:05 CDT

have you tried any other amber force field with the porting program?
I don't think it is ff99SB, and if it has a working ff99 then you
might be able to just modify that to make it 99SB.

On Sun, May 25, 2008 at 2:28 PM, Cristina Sisu <csds2_at_cam.ac.uk> wrote:
> Hello,
>
> I have downloaded the Amber 99sb force field ports for implementation in the
> gromacs program. I am trying to perform simulated annealing on a cyclic
> peptide which is cyclized by a disulfide bond between two terminal cysteine
> residues. I have named these two cysteine residues NCYX and CCYX,
> respectively, in the .pdb file to specify them both as terminal residues and
> as disulfide bonded residues. However, when I use the pdb2gmx program using
> the amber force field files this results in a system with nonphysical bonds
> (i.e. bonds are too long and the system looks like it has exploded).
>
> Any advice on implementing this amber force field in Gromacs is appreciated!
>
> Cristina
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-- 
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Carlos L. Simmerling, Ph.D.
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