Hi,
One thing to try would be to check the topology with parmed using the
checkValidity command.
-Dan
On Tue, Jul 21, 2020 at 4:57 AM angad sharma <angadsharma54.gmail.com> wrote:
>
> Dear Amber Users
>
> I am trying to run the 3D-RISM calculations using rism3d.snglpnt for a
> single frame of DNA trajectory file.
> I had a trajectory of DNA from that trajectory i took one frame of dna by
> following commands in cpptraj:-
> >parm dna.prmtop
> >trajin md100ns.nc 1 1
> >strip:WAT
> >strip:Na+
> >strip>Cl-
> >strip>MG
> >trajout dnanew.nc
> >trajoout dnanew.pdb
> >parmwrite out dnanew.prmtop
>
> And the command for 3d rism is :
> rism3d.snglpnt --pdb dnanew.pdb --prmtop dnanew.prmtop --closure KH --xvv
> ../1drism/SPC_NaCl.xvv
>
> It is giving the error:
>
> FATAL: allocation failure in ivector()
> I don't know how to remove this error, please guide me.
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Received on Tue Jul 21 2020 - 11:00:03 PDT
