AMBER Archive (2009)

Subject: Re: [AMBER] Parameter Problem

From: Manish Kumar (
Date: Wed Sep 23 2009 - 08:28:11 CDT

Thanks for you reply.
The heat3_lig.pdb is the structure I got from initial minimization and
I wanted to remove the planarity at N-H, and therefore I have chosen new
atom type for H in ALN.
Yes, I have created new atom type for 'OT' because the carbon is now SP3


On Wed, Sep 23, 2009 at 4:28 AM, FyD <> wrote:

> 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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