Re: [AMBER] Query regarding 3DRISM in Amber with CHARMM force field

From: Tyler Luchko (Lists) <"Tyler>
Date: Wed, 12 Feb 2020 10:05:06 -0800

Hi Rakesh,

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 Feb 11, 2020, at 10:46 PM, Rakesh Srivastava <> 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
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Feb 12 2020 - 10:30:02 PST
Custom Search