[gmx-users] H-Db error

[nikhil damle]

This is how i have modified the entry as i myself created the parameter file for phosphothreonine. This is normal NH hydrogen n no extra added=>directly copied from threonine. So y there is an error msg ? i added this residue in aminoacids.dat file as well. and 2ns line is tab separated. Is there any other formatting to b done ??


TPO     1
1       1       H       N       -C      CA



This is error msg i get: (I also checked h_db.c programme but could not get much help abt the error msg)
---------------------------------------------------------------
All occupancies are one
Opening library file /home/nikhil/softwares/GROMACS4.0.5/share/gromacs/top/ffG43a1.atp
Atomtype 1
Reading residue database... (ffG43a1)
Opening library file /home/nikhil/softwares/GROMACS4.0.5/share/gromacs/top/ffG43a1.rtp
Residue 97
Sorting it all out...
Opening library file /home/nikhil/softwares/GROMACS4.0.5/share/gromacs/top/ffG43a1.hdb

-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.5
Source code file: h_db.c, line: 162

Fatal error:
Error reading from file ffG43a1
-------------------------------------------------------------------------------------------


________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, 19 July, 2009 5:14:35 PM
Subject: Re: [gmx-users] H-Db error



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

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