Hi Martin,
All the latest bug fixes have been applied as i have already performed
one such calculation without any error.
I also use the other charge models (2,3) , but they all seem to give
me same charge problems (CB ~ 3 and FE ~ 4).
I am beginning to guess that there might be some problem with the
fragment because of which RESP charge fitting on the fragment is
incorrect. Could this be a problem. I would try to look into this.
Thanks and Regards
Kanika
> Hi Kanika,
>
> Have you applied all the latest bug fixes?
>
> Also, have you looked at the other options corresponding to the chg0, ..,
> chg3.bcl files.
> - 0 No constraints
> - 1 Heavy Atoms in Backbone (bb_heavy, [ca, n, c, o]) set to parm94 values
> - 2 Atoms in Backbone (bb, [ca, h, ha, n, nh, c, o]) set to parm94 values
> - 3 Atoms in Backbone plus CB (bbb, [ca, h, ha, n, nh, c, o, cb]) set to parm94
> values
>
> Options 2 and 3 may give you more reasonable numbers. BTW, option 2 is used to
> make the final parameter file.
>
> HTH,
> Martin
>
> On 6 Feb 2012, at 12:06, kanika singal wrote:
>
>> Dear AmberUsers,
>>
>> I am performing charge calculation for the metal center of a
>> metalloprotein. I have performed the gaussian charge calculation using the
>> steps explained in MCPB and i get reasonable values of Mulliken charges
>> from the gaussian log file. (attached 1fx7_ms2_large_mk.log). However, On
>> deriving the RESP charges using the standard protocol given in the tutorial
>> (respgenAdditions -> respgen -> espgen -> charge fitting), I get wierd
>> charges in the 1fx7_ms2_chg1.xml file (also attached). For eg: For CB i get
>> a charge value of ~ 3.2
>>
>> I have also checked pdb file of the metal center and it all looks OK.
>>
>> What could be the problem here ?
>>
>> Thanks & Regards,
>> Kanika
>>
>> P.S: I have attached all the required files. I would be glad to answer more
>> queries on this.
>> <1fx7_ms2_large_mk.log><1fx7_ms2_chg1.xml><1fx7_ms2_large_mk1.resp2.chg><1fx7_ms2_large.pdb>_______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Tue Feb 07 2012 - 09:00:03 PST
