[gmx-users] PRODRG server
mohsen ramezanpour
ramezanpour.mohsen at gmail.com
Mon Jan 24 15:43:15 CET 2011
Thanks for your guidance.
I looked that file,But I think the name of functional groups are different
in .rtp file because I can't find no one of them in this file.
please let me know how can I know the correct name f or functional groups
for example:HYDROXYL,CARBOXYL,HALO,AMINO and ...
Thanks in advance for your help
On Mon, Jan 24, 2011 at 4:01 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> mohsen ramezanpour wrote:
>
>> 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.
>>
>
> Please keep your story consistent. In the last message, you said you
> wanted to work completely within 53A6, so I advised you on how to do that,
> now you say that you're trying to work completely within 43A1.
>
>
> Unfortunately I can't obtain these parameter.
>>
>
> You certainly do have these parameters. 43A1 is part of the Gromacs
> installation; in the .rtp file you'll find all of the functional groups that
> were derived in 43A1, as applied to amino acids and a few other groups.
>
>
> 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!
>>
>>
> My paper that you said you read has discussion and recommendations on this
> point. But be very clear: none of the QM methods we tested were able to
> reproduce the charges that are assigned to known functional groups since the
> Gromos parameterization methodology calls for "empirical refinement." Thus,
> manual modification and thorough validation are always necessary.
>
> -Justin
>
> Thanks in advance
>>
>>
>> On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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>
>> <mailto: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> <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 <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
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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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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