[gmx-users] Regarding parametrisation

[Justin A. Lemkul]

Ravi Kumar Venkatraman wrote:
> Dear Justin,
>                  I was reading one of your literature on building 
> GROMOS-compatible small molecule topologies. I was trying to reproduce 
> the AM1BCC partial charges for the p-cresol using Antechamber from amber 
> tools version 1.5.
> 

This is a newer version than what we used in that paper (we used 1.0), so there 
may be some differences.  I understand there have been some tweaks to the QM 
programs.

> I will enlist what I have got and with literature values and gromos96 
> values. I am getting somewhat close to that but I dont know whether it 
> is right or wrong?
> 

With a different version, you may not achieve exactly what we did.  Nothing 
looks "wrong" here, per se.  Note that, as we conclude in the paper, none of the 
tested QM methods produce "correct" charges; all needed to be modified based on 
Gromos96 parameterization methodology (fitting to condensed-phase criteria).

-Justin

> CH3     AM1BCC      Literature AM1BCC    GROMOS 96
> C           0.0764                -0.0487                 
> H1         0.0004                 0.0399
> H2         0.0044                 0.0437
> H3         0.0044                 0.0437
> sum       0.0856                 0.0786                  0.0000
> 
> CH Aromatic
> C          -0.1383                -0.1381                 -0.1000
> H           0.1368                 0.1371                  0.1000
> 
> C-CH3
> C           -0.1196                -0.1123                 0.0000
> 
> COH
> C           0.1642                  0.1187                 0.1500
> O          -0.7452                 -0.4987                -0.5480
> H           0.6190                  0.4179                 0.3980
> 
> Thank you.
> 
> Ravi Kumar V
> IPC Dept.,
> IISC, INDIA.
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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