For clarity, the MCPB charges are obtained by RESP fitting to the metal cluster as a whole, in a geometrically unoptimised conformation.
This means that if you're using MCPB charges for part of the cluster, it may be better to use them for the whole cluster (including the side chains).
If you just wanted to use a CYM residue by itself, I'd use the LEaP charges.
Cheers,
Ben
On 10/10/2012, at 12:47 AM, Jason Swails wrote:
> On Tue, Oct 9, 2012 at 12:59 PM, Sangeetha B <sangeetha.bicpu.edu.in> wrote:
>
>> Dear Amber users,
>>
>> I have already posted it a few days back. Since I did not get any replies
>> yet and my query lies unsolved, I am reposting this. Sorry for the repost.
>>
>> I am using MCPB to generate prep and frcmod files for my protein with Zn2+
>> atom coordinated by HieHieCymCym motif.
>> I have successfully generated the prep and frcmod files with restraints on
>> all the backbone atoms (CA, H, HA, N, HN, C, O) to the AMBER parm99.dat
>> force field values (ChgModC).
>> When I check the charges generated finally, it is different from the ones
>> seen in $AMBERHOME/dat/leap/lib/all_amino94.lib.
>> When I compare the charges for CYM from
>> $AMBERHOME/dat/leap/lib/all_amino94.lib and
>> file:///usr/local/amber11/dat/mtkpp/amino94.xml, it is completely
>> different.
>>
>> amino94.xml (MCPB) all_amino94.lib (leap)
>>
>> N -0.46300 -0.415700
>> HN 0.25200 0.271900
>> CA 0.03500 -0.035100
>> HA 0.04800 0.050800
>> CB 0.73600 -0.241300
>> HB3 0.24400 0.112200
>> HB2 0.24400 0.112200
>> SG -0.73600 -0.884400
>> C 0.61600 0.597300
>> O -0.50400 -0.567900
>>
>>
>> Why is this difference observed? Someone suggest me which values should be
>> used for the CYM backbone atoms (including Hs).
>>
>
> The LEaP versions are 'defined' to be correct. I would use those. I don't
> know how or when the MTK++ versions were generated (or if they were even
> supposed to be the same as FF94, although I think they should be).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Oct 09 2012 - 13:30:04 PDT
