This is not an error. It is simply stating that nowhere in the parameter
database does a H-Cl bond parameter exist. This isn't terribly surprising
since it's very uncommon in biological simulations (since HCl is the only
molecule in which this would occur and it's probably not used frequently in
bio simulations).
To *fix* this, just insert the value for the bond force constant and
equilibrium distance (these should be reasonably easy to find with a little
searching).
Good luck!
Jason
On Wed, Jan 12, 2011 at 12:55 PM, <tsurma.umich.edu> wrote:
>
> Hi,
>
> I am Surma Talapatra, a 2nd year graduate student at Uiversity of Michigan,
> Chemistry, working with Prof. Eitan Geva.
> 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
> MASS
> ha 1.008 0.135
> cl 35.450 1.910
>
> BOND
> ha-cl 0.00 0.000 ATTN, need revision
>
> ANGLE
>
> DIHE
>
> IMPROPER
>
> NONBON
> ha 1.4590 0.0150
> cl 1.9480 0.2650
>
> My mol2 file is:
>
> .MOLECULE
> HCL
> 2 1 1 0 0
> SMALL
> resp
>
> .ATOM
> 1 H1 0.0000 0.0000 -1.1960 ha 1 HCL 0.266541
> 2 Cl1 0.0000 0.0000 0.0700 cl 1 HCL -0.266541
> .BOND
> 1 1 2 1
> .SUBSTRUCTURE
> 1 HCL 1 TEMP 0 **** **** 0 ROOT
>
> Surma Talapatra
>
> Graduate Student
>
> Chemistry
>
> U Michigan
>
> On Wed, 12 Jan 2011 09:48:24 -0800, amber-request.ambermd.org wrote:
> > Welcome to the AMBER.ambermd.org mailing list!
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Jan 12 2011 - 10:30:03 PST
