Re: [AMBER] error in 3d rism calculation

From: Tyler Luchko (Lists) <"Tyler>
Date: Mon, 20 Jul 2020 13:25:09 -0700

Hi Angad,

Check to see if the prmtop has periodic boundary conditions. You can tell by looking in the prmtop for


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,


> On Jul 20, 2020, at 10:27 AM, angad sharma <> wrote:
> I'm trying to calculate the 3d RISM of dna in NaCl with concentration
> 0.005M. Here is my input file for 3drism:-
> rism3d.snglpnt --pdb dnanew.pdb --prmtop dnanew.prmtop --closure kh --guv
> dnanew --xvv ../1drism/SPC_NaCl.xvv
> after submitting this input file i got a error, here it is that error
> Running MME
> FATAL: allocation failure in ivector()
> I don't know how to correct this error.
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Mon Jul 20 2020 - 13:30:02 PDT
Custom Search