[gmx-users] PRODRG server

[Justin A. Lemkul]

mohsen ramezanpour wrote:
> Dear Justin
> 
> I read your articles about PRODRG server,they were very useful.
> But I have a question:
> are charges of functional groups and generally other atom groups the 
> same in all force fields?
> Because you have modified charges of your molecules by Gromos96 53A6 
> while prodrg server is generating topology files in 43A1.
> I want to know can I replace charges from gromos 53A6 or other forcefields?
> thanks in advance
> 

Charges are not the same between force fields.  We did our study with 43A1 since 
that is what PRODRG purports to produce.  I would say that our recommendations 
carry to other Gromos force fields, as well, but don't take charges from 43A1 
and apply them to 53A6.  Be consistent within the force field.

The atom types produced by PRODRG are largely shared between 43A1 and 53A6, so 
if you *completely* replace all charges with those from 53A6, you should have a 
topology that is compatible with 53A6.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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