Dave Segala wrote:
Hi all,
I am using the opls-aa force field to simulate my molecule. I have files
which ran correctly on version 3.2.1 and are not running on version 3.3.
When I use the command pdb2gmx I encounter many errors:
1. wrong input on ffolpsaa.hdb file
2 7 OW
when I change to 2 7 HW OW, it works.
2. in the -c and -n .tdb files there are only supposed to be 4 entries in
[replace] and in [add] 3 entries on the second line.
After changing only these files an atom is not found where combining the
.tdb and .rtp files to create the .top file.
Does anyone have any suggestions on how to fix these problem or where to
look.
Cheers,
Dave
the format of the hdb file has changed, and new files are provided. the
same goes for the tdb files: the name of the atom to replace has to be
added. If you have added stuff to your old files, you can by comparing
the standard 3.2 and 3.3 files, deduce how to make your changes work
with 3.3.
--
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 [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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
