Re: [AMBER] parmchk

From: David A. Case <>
Date: Wed, 12 Jan 2011 13:25:46 -0500

On Wed, Jan 12, 2011, wrote:

> I am using AMBER10 to create a system of HCl molecules. I used gaussian
> (g03) to give charges to HCl pdb file. Then I converted the .gout file to
> .mol2 file using antechamber. Then I used parmchk to get the frcmod file,
> but I am getting a strange error in the parmchk file:
> remark goes here
> ha 1.008 0.135
> cl 35.450 1.910
> ha-cl 0.00 0.000 ATTN, need revision

This means that prmchk doesn't know how to create a force field for H bonded
to Cl. You will have to edit that line to put in the correct parameters
yourself (e.g. from Herzberg's book).

> ha 1.4590 0.0150
> cl 1.9480 0.2650

You should also think about whether the above values are correct or not.
Antechamber was designed for "organic" molecules, and it is unlikely that what
it comes up with for HCl is optimal. See if there are some literature values
around, and just edit the frcmod file above.

..good luck...dac

AMBER mailing list
Received on Wed Jan 12 2011 - 10:30:04 PST
Custom Search