[gmx-users] Human Serum Albumin problem

Sampo Karkola Sampo.Karkola at helsinki.fi
Wed May 9 09:26:10 CEST 2007

Hi George,

you should read the publication carefully. Also in the pdb file it says 
that there are missing residues and missing atoms in some residues (eg 
HIS3). As mentioned many times in the list, you should not use the 
-missing option unless you want to simulate broken system (usually you 
don't). You can add the missing atoms and residues with some molecular 
modelling software.



George Abadir wrote:
> Hi,
>     I have downloaded the 1HA2.pdb (describing human serum albumin) file 
> from www.pdb.org and ran pdb2gmx to make a topology file for it. I got 
> an error message "Source code file: hizzie.c, line: 267
> Fatal error: Incomplete ring in HIS1". I also tried the '-missing' 
> option and '-ignh' option but still that didn't work. Does anybody know 
> what it means and how to get around it?
>    Thank you very much in advance,
> Regards,
> George
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Sampo Karkola, M.Sc.
Research scientist
Teaching assistant

Laboratory of Organic Chemistry
Department of Chemistry
Faculty of Science
PO Box 55 (A.I. Virtasen aukio 1)
FIN-00014 University of Helsinki

tel +358 9 19150369, fax +358 9 19150366

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