[gmx-users] GAAMP parameterization
David van der Spoel
spoel at xray.bmc.uu.se
Tue May 2 07:06:23 CEST 2017
On 02/05/17 06:06, Mohsen Ramezanpour wrote:
> Hi Everyone,
> I would like to know your opinion on these questions.
> I highly appreciate your comments in advance.
You could at least at the address of the server and tell in one line
what it is supposed to do.
You should never mix force fields unless you really really know what you
are doing. Not even change water models - most people trying that don't
really know what they are doing.
> On Thu, Apr 27, 2017 at 10:23 PM, Mohsen Ramezanpour <
> ramezanpour.mohsen at gmail.com> wrote:
>> Dear Gromacs users,
>> Using GAAMP server for parameterization, if the GAFF for
>> "initial parameters" is used instead of "CGenFF":
>> 1) Can the results still be used for using simulation in "Charmm36" force
>> field? Assuming that all the other values are chosen as default ones in the
>> GAAMP webpage.
>> 2) Will the result be the same (or approximately the same) with when
>> "CGenFF" is used as initial parameters?
>> 3) Will the units for angles, dihedrals, distances, ... be in CGenFF or
>> GAFF? I was wondering if I can still use the cgen_charmm2gmx.py script for
>> conversions to use it in Gromacs package?
>> As I understood from the paper, GAAMP can give output for parameterization
>> in both Charmm and Amber force fields.
>> This could be easily tested by running the same job two times.
>> Unfortunately, GAAMP server has some problems at the moment so it will take
>> too much time to check this.
>> I appreciate your comments in advance.
>> *Rewards work better than punishment ...*
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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