Gaurav Chopra wrote:
Hi
I am getting the following error with mdrun. I have done a few things
but the system complains of 1-4 interactions and gives LINCS warning if
the constraints are not turned off in the mdp file. I also changed the
fudgeQQ = 1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun but I
get 1-4 interaction table size error and then LINCS warning. The output
of mdrun for one of these peptides is as follows. I am working on normal
mode decoys of each peptide and many of the decoys have no problems with
mdrun but some gives this error and Segmentation Fault.
Please advice.
you need to minimize better, but if your structures are really bad it
won't help either (e.g. when you have a sidechain sticking through a ring)
--
David.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
