[gmx-users] Regarding the charge of the atom in the .rtp file

[Justin Lemkul]

On 6/22/17 11:23 AM, Dilip H N wrote:
> No, its not related to parameterization methodology. it is a different
> question...
> 
> how can i identify the molecule as methylamine (for example) since in the
> .rtp the molecule type is written as [MAM1]
> [ MAM1 ]
>    [ atoms ]
>     N1 NG321        -0.990  0
>     C1 CG3AM2     -0.060  1
>    HN1 HGPAM2    0.390  2
>    HN2 HGPAM2    0.390  3
>    HC1 HGAAM2    0.090  4
>    HC2 HGAAM2    0.090  5
>    HC3 HGAAM2    0.090  6
>    [ bonds ]
>     N1    C1
>     N1   HN1
>     N1   HN2
>     C1   HC1
>     C1   HC2
>     C1   HC3
> Is thr any hint such tht i can identify the molecule type written in .rtp
> file.??
> Or should i manually find it out..??... but in case of Glycine the molecule
> type is [GLY] which is easy to find....
> How can i solve this issue..??
> 

You need to go to the original CHARMM force field files.  These include names 
and (typically) chemical structure drawings.

http://mackerell.umaryland.edu/charmm_ff.shtml#charmm

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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