abhigna polavarapu wrote:
I am running a 10ns simulation on a 42 mer peptide. I am doing this for
predicting the stability of the beta sheet. So I deleted a bond called
the lactame bond between two amino acids Lys and Asp. So if I just
create mutation at any other position in the beta sheet the mdrun
crashes with an error saying that 1-4 interaction between the residues
in Lys is greater than the size of the box. Increase the table
extension. This seems like system is exploding. But if I mutate those
two amino acids to Ala I am not getting that error. So please help me
with this. As I need to analyse lots of mutations othen than mutation
those two amino acids
Thank you
abhigna
------------------------------------------------------------------------
_______________________________________________
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
search the archives.
your structure is bad.
--
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
