[gmx-users] H-Db error

[Justin A. Lemkul]

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 <Mark.Abraham at anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *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

========================================