[gmx-users] Error when adding a unnatural amio acid

[Mu Yuguang (Dr)]

Please check the xlateat.dat file in share/top/
There is one line in it

protein  HT1    H1

which will automatically change your atom name "HT1" to H1.

Best regards
Yuguang
 
Dr. Yuguang Mu
Assistant Professor
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive  Singapore 637551 Tel: +65-63162885 Fax: +65-67913856
http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php
 
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yang Ye
Sent: Wednesday, January 03, 2007 9:57 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Error when adding a unnatural amio acid

You may try add residue name ASO to the end of /top/aminoacids.dat and 
also increment the number on the top.

Regards,
Yang Ye

On 1/3/2007 8:55 AM, yuemin liu wrote:
> Hi, Everyone,
>
> I got Error when adding a unnatural amio acid in a
> protein. I have all the rtp and hdb file modified
> using information either from ffgmx.rtp ffgmx.hdb or
> thr rtp file form progdrg. There is no H1 in either
> rtp file or my new pdb file. When I try use pdb2gmx to
> generate top file, it always give the error message
> following;
> "Atom H1 not found in rtp database in residue ASO, it
> looks a bit like H". I know it refers to the Hydrogen
> of the peptide bond which has nothing wrong there.
>
> Hope can get help from you with this,
>
> Thanks,
>
>
>
>
>
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