[gmx-users] new residue in the rtp fiels

David spoel at xray.bmc.uu.se
Sat Jun 19 08:34:57 CEST 2004

On Fri, 2004-06-18 at 21:18, Marcela P.Aliste wrote:
> Hi :
> I added new residues in the ffG43a2.rtp file and included in the
> aminoacid.dat and in
> the ffG43a2.hdb. This new residues are for the N-terminal and the
> C-terminal part of 12 separated alpha helices.
> I did this before with no problem to run distances restraint between
> the different helices.
> I modified some of the helices and include the new n and c-terminal.
> I got the following problem using pdb2gmx in the new structures
> Fatal error: Atom O in residue LEC 21 not found in rtp entry with 10
> atoms	while sorting atoms.
> I checked : the name, the number and order of the atoms in the pdb and
> in the rtp.
> This residue is the last one in the first helices.
> I modified and included these residues in the aminaocid.dat ffG43a2.rtp
> and in the ffG443a2.hdb
> Is there another file to modify?
> Could be the problem that is trying to connect the last residue with
> the first of the next helix?
No, my guess is that it is trying to put a terminus (e.g. COO-) on it.
Run pdb2gmx -ter

> Thanks a lot
> Marcela P. Aliste
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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://xray.bmc.uu.se/~spoel

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