[gmx-users] problem with selenomethionine residues

Sridhar Acharya sridharfirst at gmail.com
Tue Jun 13 11:37:10 CEST 2006

When I am running the mdrun for position restrain the program terminates 
giving the following error. The protein molecule contains 16 selenomethionine residues,
the topology for which was got from the PRODRG server.

When run in GROMACS 3.2.1 version
Wrote pdb files with previous and current coordinates
Fatal error: ci = -2147483648 should be in 0 .. 6782 [FILE nsgrid.c, LINE 

When run in GROMACS 3.3.1 version
Fatal error:
Too many LINCS warnings (12461) - aborting to avoid logfile runaway.
This normally happens when your system is not sufficiently equilibrated,or 
if you are changing lambda too fast in free energy simulations. 
If you know what you are doing you can adjust the lincs warning threshold 
in your mdp file, but normally it is better to fix the problem.

Looking forward for ur response,


Sridhar Acharya, M
Senior Research Fellow
Lab of Computational Biology
CDFD, Gandipet Campus
Hyderabad. AP. INDIA
email: sridhar at cdfd.org.in
Phone: Lab: 08413-235467*2044
Mobile: 9866147193

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