[gmx-users] PRODRG server

[mohsen ramezanpour]

Ok
then,I can use  PRODRG server to generate .top and .gro files for drug.
since it's reported charges are not very accurate ,we can replace all
charges completely with them in 53A6(if was present).
But it means we are working in 53A6 force field.
then,we must generate .top and .gro files for our protein with 53A6 too.
and work completely with 53A6.
Am i right?
thanks in advance

On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ========================================
>
> 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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