Thanks, Tyler for your kind help.
Rakesh Srivastava
Research Fellow
School of Computational & Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067
India
On Wed, Feb 12, 2020 at 11:36 PM Tyler Luchko (Lists) <
tluchko.lists.gmail.com> wrote:
> Hi Rakesh,
>
> Check to see if the prmtop has periodic boundary conditions. You can tell
> by looking in the prmtop for
>
> %FLAG BOX_DIMENSIONS
>
> 3D-RISM doesn’t care about this information but the SFF library that is
> also used seems to have problems with it.
>
> To get rid of this information, make sure to use the 'nobox’ flag when
> stripping solvent. If the solvent is already removed, you can get rid of
> the box information with the command
>
> strip ‘’ nobox
>
> Hope this helps,
>
> Tyler
>
> > On Feb 11, 2020, at 10:46 PM, Rakesh Srivastava <allahabad.21.gmail.com>
> wrote:
> >
> > Dear Amber users,
> > I have a small protein of 34 residues, There are two unusual amino acids
> > whose CHARMM force field parameters were used and MD simulation was
> > performed on GROMACS with the CHARMM36 force field. Then I converted the
> > trajectory into Amber trajectory using MD convert tool and prepared the
> > prmtop file using parmed.
> > The MMPBSA calculation is running fine with new trajectory and prmtop
> file
> > in Amber but when I am trying to run the 3DRISM calculation, I get
> > following error:
> >
> > Running MME
> > FATAL: allocation failure in ivector()
> >
> > Can anyone help me out here?
> >
> > Thanks in advance.
> >
> > Rakesh Srivastava
> > Research Fellow
> > School of Computational & Integrative Sciences
> > Jawaharlal Nehru University, New Delhi-110067
> > India
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> > AMBER.ambermd.org
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>
>
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Received on Fri Mar 06 2020 - 22:30:01 PST
