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

David van der Spoel spoel at xray.bmc.uu.se
Wed Jan 3 08:50:37 CET 2007

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,
And by the way, avoid using ffgmx. Search archives for reasons why.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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