I think there may be some problem with the topology dnanew.prmtop. You can
generate the topology with no box information.
You just need to load the pdb file that you have extracted from the DNA
trajectory file in tleap and generate the new topology file.
tleap
source forcefield for dna
dna=loadpdb dnanew.pdb
saveamberparm dna dna.prmtop dna.crd
quit
I hope this will solve your problem.
On Tue, Jul 21, 2020 at 2:27 PM 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 - 05:00:03 PDT
