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