From the archives, a simple search for "43b1 4.0":
http://www.gromacs.org/pipermail/gmx-users/2008-December/038463.html
-Justin
Anirban Ghosh wrote:
Hi ALL,
I want to do a MD simulation of a GPCR protein using GROMACS vacuum force field. I want to use the old force field G43b1 (vacuum simulation)
which is not there in GROMACS4.0.3. I would like to know which is the substitute for this G43b1 force field
from the present menu:
Select the Force Field:
0: GROMOS96 43a1 force field
1: GROMOS96 43a2 force field (improved alkane dihedrals)
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
4: GROMOS96 53a6 force field (JCC
2004 vol 25 pag 1656)
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
6: [DEPRECATED] Gromacs force field (see manual)
7: [DEPRECATED] Gromacs force field with hydrogens for NMR
8: Encad all-atom force field, using scaled-down vacuum charges
9: Encad all-atom force field, using full solvent charges
Should I use the 8th one? The new manual for GROMACS4.0 also does not reflect
this change.
Any suggestion is welcome.
Regards,//
//
*Anirban Ghosh*
*Grade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India
*
------------------------------------------------------------------------
Share files, take polls, and make new friends - all under one roof.
Click here.
<http://in.rd.yahoo.com/tagline_groups_8/*http://in.promos.yahoo.com/groups/>
------------------------------------------------------------------------
_______________________________________________
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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
