Hi Daniel,
Thanks for your reply. I developed it with antechamber and of course I ran
parmchk that's why I got the frcmod to create the prmtop. I used following :
antechmaber -i pdbfile -fi pdb -o mol2file -fo mol2 -rn FAD -at gaff -c
bcc -j 5 and afterward
parmchk2 -i mol2file -f mol2 -o frcmodfile -a Y .
Then used leap and so on...and got the solvated prmtop and inpcrd files
with FAD and protein complex. I ran the minimisation1 with restraint and
got no error (possible reason, I fixed the structures including FAD), then
removed the restraint and got the 1-4 ELE error. When I fixed FAD only,
all simulations including minimisation, heat, density, equlibrations,
production..everything run fine. What I guess, relaxing the FAD, angle
between P-O-P decreases which is bringing the atoms closer and giving the
1-4 ELE error.
So please help me to solve this issue.
Regards
Kshatresh
On Thu, Jan 15, 2015 at 6:35 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> We need way more information. What parameters are you using for
> adenine dinucleotide? Did you obtain them from somewhere or did you
> develop them yourself (and if so, how)? If you developed parameters
> with antechamber did you run parmchk afterwards? What does your tleap
> script look like?
>
> -Dan
>
> On Thu, Jan 15, 2015 at 8:17 AM, Kshatresh Dutta Dubey
> <kshatresh.gmail.com> wrote:
> > Dear Users,
> >
> > I am simulating flavin adenine dinuecleotide complex. During the
> > minimisation, the atoms neighbouring to two phosphorus of FAD, stack
> > together and are giving 1-4 ELE errors. However the parameterized
> structure
> > of FAD looks fine in leap. I have attached two snapshots before and after
> > minimisation which may clear my issue.
> > I will be very thankful for every suggestion to fix the problem.
> >
> > Regards
> > Kshatresh
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With best regards
************************************************************************************************
Kshatresh Dutta Dubey
Post Doctoral Researcher,
Lise Meitner Center for Computational Quantum Chemistry
Hebrew University of Jerusalem Israel
Jerusalem, Israel
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 15 2015 - 09:30:04 PST
