[gmx-users] PRODRG server
ramezanpour.mohsen at gmail.com
Mon Jan 24 12:06:28 CET 2011
Actually by doing this we are using two different force fields in one
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
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
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:
>> 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...
>> 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
>> 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 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
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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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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