AMBER Archive (2009)

Subject: Re: [AMBER] Parameter Problem

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Sep 23 2009 - 03:28:49 CDT

Dear Manoj,

> I have developed parameter for an modified amino acids. The lib files and
> frcmod files are attached with the mail (in zipped folder).
> After heating and minimization and heating, the structure of peptide does
> not look reasonable (Please try to have a look to the structure).
> The minimization and heating was performed in TIP3P water box.

This is difficult to answer to your problem; "does not look
reasonable" is not precise... I looked at your frcmod file and aln &
lec libraries. Your PDB file heat3_lig.pdb looks bad. Is it the
structure you obtained after geometry optimization ?

With do you have this ALN fragment since it looks like as the regular
ALA fragment ?

It looks like you created a new atom type OT for a carbonyl oxygen in
a terminal COOH group in the LEC library... If so, the O2 atom type
should be OK.

regards, Francois

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