[gmx-users] Fwd: Can you help me? (Problem with simulating two peptides -TAW-)

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jul 3 13:42:39 CEST 2007

Fufeng Liu,

Please keep discussions on the list... And give a subject line that
covers the topic of the mail.


---------- Forwarded message ----------
From: fufengliu at tju.edu.cn <fufengliu at tju.edu.cn>
Date: Jul 3, 2007 11:12 AM
Subject: Can you help me?
To: tsjerkw at gmail.com

Dear Tsjerk:
I want to simulate two peptides, which have same sequences. I try the following
methods, but they didn¡¯t work.
1. I put two peptides in a file using SYBYL software, But GROMACS
think them as a
protein. So LINCS warning turned up and 1-4 interactions also showed up and the
simulation crashed.
2. I found some suggestions from GROMACS Mailing List and I tried giving chain
identifiers. But it doesn¡¯t work. I think I didn¡¯t add chain identifier. Can
tell me how to add chain identifier? Can you tell me how to do it?
3. I build the two topologies on separate files and combine them, but
get the same
error as the first method.
Can you tell me how to treat detailedly? Thank you in advance!
Best Regards!
Fufeng Liu

Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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