This is really a question for the Gromacs mailing list:
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
Maybe try building with tleap and minimizing with sander and see if
you get the same behavior?
-Dan
On Wed, Jul 13, 2016 at 12:14 AM, Atila Petrosian
<atila.petrosian.gmail.com> wrote:
> Hi,
> I have a problem after this step:
>
> grompp -f em.mdp -c sol_ions.gro -p topol.top -o em.tpr
> mdrun -v -deffnm em
>
> I achieved the ligand parameters from ANTECHAMBER that are usable for
> GROMACS software.
> After using this command line :
>
> $AMBERHOME/exe/ambpdb -p lig.prmtop < lig.inpcrd > lig.pdb
>
> The pdb structure of ligand visualized with VMD and it was OK, but after
> minimization step when I see em.gro and em.trr file in VMD I saw that the
> structure of ligand in a protein is broken and a series of unusual bonds
> are fromed.
>
>
> Apparently all parameters are correct and I don't have any Warning or Notes
> in each steps but I don't know where the problem is in this stage.
>
> I'm really appreciate if you could help me,
>
> Regards,
>
> Yeganeh
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> 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)
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Received on Wed Jul 13 2016 - 07:30:02 PDT
