nikhil damle wrote:
Hello,
Thanks for the reply. I am trying to add N-H hydrogen of a residue which
is tab separated formate; just like other residues. if i remove this H
from .hdb file, file can be read and pdb2gmx gives missing atom error.
But when i have it in the file, it can not read it. if there were
version related problem, it should give same error even after removing
this H. i m using Gromacs-4.0.5 on linux machine. so no OS related
problems possible
Did you properly increment the line indicating how many entries pdb2gmx should
find in that section? For example, if I'm playing around with Asn, and adding
some H somewhere:
ASN 2
becomes
ASN 3
before pdb2gmx can properly handle the addition.
It would be helpful to see the exact error message.
-Justin
Regards,
Nikhil
------------------------------------------------------------------------
*From:* Mark Abraham <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*Sent:* Sunday, 19 July, 2009 2:43:05 PM
*Subject:* Re: [gmx-users] H-Db error
nikhil damle wrote:
> Hi,
> I added peptide H to the the new residue i added to .rtp file in the
ffG43a1.hdb file But the pdb2gmx gives error saying it can not read hdb
file. If i remove this H from .hdb file, it gives error of missing atom.
How should i resolve this problem ? y can pdb2gmx not read hdb file if i
add one extra H ??
If your version of the .hdb file can't be read, then you've broken the
format (see chapter 5), or created a file that does not adhere to the
right conventions (e.g. by having Windows-style line endings - fix using
dos2unix utility), or mangled the file permissions, or quite a few other
possiblities.
Mark
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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