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 <jalem...@vt.edu
<mailto:jalem...@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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@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!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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@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!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
