[gmx-users] error in ffG43a1p force field

[jimkress_58]

He didn't have a CC: to smithgr at cancer.org.uk so he probably felt he had to
resubmit the question,  LOL.

Jim

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: Friday, July 24, 2009 7:22 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] error in ffG43a1p force field



Thamu wrote:
> Hi,
> 
> i am trying to run md for protein-peptide complex. the peptide has
> phosphorylated tyrosine.
> 
> i got the following error when i run pdb2gmx
> 
> Fatal error:
> Error in hdb file ffG43a1p.hdb:
> Wrong number of control atoms (2 iso 3) on line:

So, did you follow Mark's advice and read section 5.6.2?  Repeating a
question 
without reference to previous help is usually a fast way to get ignored. 
Demonstrate that you are willing to help yourself before you expect to get
more 
free help :)

This is indeed a formatting issue.  The ffG43a1p force field was designed
for 
use with Gromacs-3.1.x, when formatting of these files was slightly
different. 
They are quite easy to fix, if you read the manual.

-Justin

>    1    1    N    -C    CA
> 
> I also tried with phosphoserine, i got the same error as for 
> phosphotyrosine.
> I am using gromacs-4.0.2.
> 
> 
> I would greatly appreciate if some one help me to solve this error.
> 
> Thanking you,
> 
> Yours sincerely,
> Thamu
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

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

========================================
_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php