Re: [AMBER] Difference between frcmod and mdl parameters

From: David A Case <>
Date: Fri, 22 Jun 2018 14:02:29 -0400

On Fri, Jun 22, 2018, Rakesh Srivastava wrote:

> Can anyone please tell me that why size and epsilon parameters for ions
> (like Na+) in the frcmod
> file and the mdl file (which is used in rism1d) are different. Actually,
> the size difference is not only of a factor of 2^(1/6) and epsilon values
> are quite different (though units in both are kcal/mol mentioned in manual).

Could you be specific about exactly which files you are comparing?

If I look for the Joung-Cheathm Na+ ions associated with SPCE water,
here is what I find:

1. In $AMBERHOME/dat/rism1d/mdl/c_SPCE/Na+.mdl:


2. In $AMBERHOME/dat/leap/parm/frcmod.ionsjc_spce:

  Na+ 1.212 0.3526418

These agree perfectly. If there are other pairs of files that seem to be in
disagreement, please let us know.


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Received on Fri Jun 22 2018 - 11:30:02 PDT
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