[gmx-users] PRODRG server

[mohsen ramezanpour]

Dear  Dr.justin
Actually by doing this  we are using two different force fields in one
simulation.
I had done it before and the result was that I discussed before in
gmx-users(LINCS Error,Exploding system,Bad contacts between atoms)
Then,this approch seems to doesn't work about my system.

Then I  want to find charges and charge groups for gromos 43A1 and replace
them for my drug(to edit PRODRG file manually) and work totally in gromos
43A1.
Unfortunately I can't obtain these parameter.
Please let me have if you have it.
Can I use some Ab Initio software for determining partial charges of my
drug?
for example ABINIT or Gaussian!

Thanks in advance

On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> mohsen ramezanpour wrote:
>
>> 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
>>
>
> That sounds like a reasonable approach.  Be sure to validate the drug
> topology.  In my experience, this procedure is pretty good, but you always
> have to convince reviewers...
>
> -Justin
>
>
>> On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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 <http://vt.edu> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/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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