Hi Angad,
I tried sending this email the other day but it seems it never went through.
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 Jul 21, 2020, at 10:34 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
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 Wed Jul 22 2020 - 10:00:04 PDT
