On 18/06/2011 1:13 AM, udaya kiran marelli wrote:
Dear GROMACS users,
I am trying to construct a cyclic hexa peptide containing all Ala
residues. During pdb2gmx conversion using the command (pdb2gmx -ff
charmm27 -ignh -f TESTALA.pdb -o TESTALA.gro -ter) it gave the
following error while I am demanding the program to give uncharged
termini (option : None)
WARNING: atom HN is missing in residue ALA 1 in the pdb file
You might need to add atom HN to the hydrogen database of
residue ALA
in the file ff???.hdb (see the manual)
With -ignh you told it to strip away all the H atoms, and that requires
that pdb2gmx knows how to rebuild them (or doesn't need to know).
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.5
Source code file: pdb2top.c, line: 704
Fatal error:
There were 1 missing atoms in molecule Protein, if you want to use
this incomplete topology anyhow, use the option -missing
In the .hdb file the atom HN is defined already. The error is that it
is removing the #HN# atom from the Ala 1 residue at the cyclization point.
If you mean that the the cyclization is achieved with a peptide bond
from "N-terminal" N to "C-terminal" C, you will have to use the
specbond.dat mechanism to achieve that. See chapter 5.
The problem arises because HN is defined in the .hdb in terms of C in
the preceding residue, which is not applicable in your case, because
there is not a regular peptide bond.
Rather than the "brute force" -ignh mechanism, there may be a better
approach (like removing particular offending hydrogen atoms from your
input coordinate file) that doesn't require pdb2gmx to need to know how
to rebuild HN.
Mark
Could you suggest me in getting rid off the problem.
yours sincerely
Uday.
Marelli Udaya Kiran
C/o. Professor Dr. Horst Kessler
Institute for Advanced Study
Department Chemie
Technische Universität München
Lichtenbergstrasse 4
D-85747 Garching, Germany
Tel.: +49-(0)89-289-13760 <tel:%2B49-%280%2989-289-13760>
Fax: +49-(0)89-289-13210 <tel:%2B49-%280%2989-289-13210>
email: kiran.ud...@tum.de <mailto:kiran.ud...@tum.de>
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