[gmx-users] [Fwd: problem in grompp]

David spoel at xray.bmc.uu.se
Wed Aug 31 17:24:32 CEST 2005

-------- Forwarded Message --------
From: poor nima <poornings at yahoo.co.in>
To: David <spoel at xray.bmc.uu.se>
Subject: problem in grompp
Date: Wed, 31 Aug 2005 09:08:40 +0100 (BST)
 Dear  David,
Sorry for disturbing you. I have two more problems.
This is my first problem:
I am doing protein simulation with hexane and water. 
earlier I did simulations with gromacs version 3.1.4. But now I am doing
simulation with version 3.2.1. 

When I run a simulation  in grompp step it shows error that atom type
‘K’ not found. Why this version showing this kind of error because
I haven't got this problem in version 3.1.4.  

I have edited my pdb by removing the water molecule. Yet it is showing
this problem.

this is my another problem:

I want to run the protein simulation with all hydrogen atoms. In version
3.1.4 there is an option to fix a forcefield (that is  option 1 ffgmx2).
This Forcefield is specifically for proteins with all hydrogens. In this
version(3.2.1) I am giving option 5.

When I run the protein using version 3.2.1 it shows some error in the
321 aminoacid and giving option to ignore hydrogen.   I need simulation
with hydrogen. Please help me to sort out this problem.

Am I giving the correct forcefield? or should I change it? If I have to
change the Forcefield what should I give? Or This problem might be some
other reasons? and please help me to sort out this problem.

Thanks in advance.

With regards,



Studentship Trainee, 
Bioinformatics Center,
School of biotechnology,
Madurai Kamaraj University,
E.MAIL: poornings at yahoo.co.in. 

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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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