Anirban Ghosh wrote:
Thanks a lot Justin for the reply.
I have already seen that post. But the problem is that there is no clear
answer in it. Hess says that there NO G43b1 force-field now in GROMACS
and G43b1 was just a modified version of G43a1 but with no residue
charges. So this means that there in no vacuum force-field in GROMACS
now or can I use any of other 8 force-fields for this purpose? Please
rectify if I am wrong and please tell me force-field number which has
the same properties as G43b1. What are following two force-fiels used for:
6. [DEPRECATED] Gromacs force field (see manual)
8. Encad all-atom force field, using scaled-down vacuum charges
The "Gromacs force field" should not be used for anything (hence, "deprecated").
I am not terribly familiar with Encad, but I do not often see it in the
literature.
Within the thread that I posted were several opinions on how you can continue.
The other question to ask yourself is - what do others use in similar
situations? Check the literature.
-Justin
There is no description in the GROMACS4 manual or the pdb2gmx man page.
Please update the information.
Regards,
*Anirban Ghosh*
*Grade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India
*
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--
========================================
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
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