Hi Jason,
Thank you so much for your help!
~Surma Talapatra
On Wed, 12 Jan 2011 13:26:15 -0500, Jason Swails <jason.swails.gmail.com>
wrote:
> 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:
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Received on Wed Jan 12 2011 - 11:00:03 PST
