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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 07 2012 - 06:30:04 PST
