[gmx-users] Re: Replacement for G43b1 force field?

[Justin A. Lemkul]

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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-- 
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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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