I have attached all the files required for running the MCPB charge
calculations. The original zip file I sent was too large and was rejected by
the amber list. I'll try this again... I use run.MCPB.csh to run all the
programs. I modified the genMetalFF.sh from the original so that it adds a
few extra lines to the settings file (i.e. non-standard libraries). Please
let me know if you require any further information.
Hashem
On Wed, May 25, 2011 at 7:20 AM, Hashem Taha <htahaphd.gmail.com> wrote:
> Hi Martin,
>
> I have attached a zip file that contains all the files required for running
> the MCPB calculations. I use run.MCPB.csh to run all the programs. I
> modified the genMetalFF.sh from the original so that it adds a few extra
> lines to the settings file (i.e. non-standard libraries). Please let me know
> if you require any further information.
>
> Hashem
>
> On Wed, May 4, 2011 at 4:02 AM, Martin Peters <martin.b.peters.me.com>wrote:
>
>> Hi Hashem/Ben,
>>
>> Could you send us the bcl scripts you used to generate the resp files?
>>
>> Regards,
>>
>> Martin.
>>
>> On 3 May 2011, at 22:21, Ben Roberts wrote:
>>
>> > Hi Hashem,
>> >
>> > On 3/5/2011, at 11:51 a.m., Hashem Taha wrote:
>> >
>> >> Hi Ben,
>> >>
>> >> Thanks for the response. Sorry, I was away and didn't have a chance to
>> >> read your message. I have attached the RESP input files that MCPB
>> >> generates (i attached the input with no restraints). The charges on the
>> >> individual residues are GLU (-1), ASP (-1), KCX (-1), MOH (-1), ZN1
>> (2+),
>> >> ZN2 (2+), and the rest are 0. The overall charge on the model is 0.
>> >> However, I would like the RESP charges on ZN and not the formal 2+
>> charge.
>> >
>> > OK, I'll take a look at those files and get back to you.
>> >
>> > Regards,
>> > Ben
>> >
>> > --
>> > For greater security, I support S/MIME encryption.
>> >
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>>
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Received on Wed May 25 2011 - 09:30:05 PDT
