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On 18/06/2011 1:13 AM, udaya kiran marelli wrote:
<blockquote
cite="mid:BANLkTikpHYWX3Vf2irw7zZyF00VDwM5qyw@mail.gmail.com"
type="cite">
<div class="gmail_quote">
Dear GROMACS users,<br>
<br>
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)<br>
<br>
WARNING: atom HN is missing in residue ALA 1 in the pdb file<br>
You might need to add atom HN to the hydrogen database
of residue ALA<br>
in the file ff???.hdb (see the manual)<br>
</div>
</blockquote>
<br>
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).<br>
<br>
<blockquote
cite="mid:BANLkTikpHYWX3Vf2irw7zZyF00VDwM5qyw@mail.gmail.com"
type="cite">
<div class="gmail_quote">
-------------------------------------------------------<br>
Program pdb2gmx, VERSION 4.0.5<br>
Source code file: pdb2top.c, line: 704<br>
<br>
Fatal error:<br>
There were 1 missing atoms in molecule Protein, if you want to
use this incomplete topology anyhow, use the option -missing<br>
<br>
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.<br>
</div>
</blockquote>
<br>
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.<br>
<br>
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.<br>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTikpHYWX3Vf2irw7zZyF00VDwM5qyw@mail.gmail.com"
type="cite">
<div class="gmail_quote">
Could you suggest me in getting rid off the problem.<br>
<br>
<br>
yours sincerely<br>
Uday.<br>
<br>
Marelli Udaya Kiran<br>
C/o. Professor Dr. Horst Kessler<br>
Institute for Advanced Study<br>
Department Chemie<br>
Technische Universität München<br>
Lichtenbergstrasse 4<br>
D-85747 Garching, Germany<br>
<br>
Tel.: <a moz-do-not-send="true"
href="tel:%2B49-%280%2989-289-13760" value="+498928913760">+49-(0)89-289-13760</a><br>
Fax: <a moz-do-not-send="true"
href="tel:%2B49-%280%2989-289-13210" value="+498928913210">+49-(0)89-289-13210</a><br>
email: <a moz-do-not-send="true"
href="mailto:kiran.udaya@tum.de">kiran.udaya@tum.de</a><br>
</div>
<br>
</blockquote>
<br>
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