[gmx-users] Warning: atom is missing in residue

[Justin Lemkul]

On 2/14/14, 7:30 PM, ehs wrote:
> Thanks Justin. But I found some residue int the rtp file which have more than
> one residue inside them such as:
>
> [ TYR ]
>   [ atoms ]
>      N     N    -0.31000     0
>      H     H     0.31000     0
>     CA   CH1     0.00000     1
>     CB   CH2     0.00000     1
>     CG     C     0.00000     1
>    CD1     C    -0.14000     2
>    HD1    HC     0.14000     2
>    CD2     C    -0.14000     3
>    HD2    HC     0.14000     3
>    CE1     C    -0.14000     4
>    HE1    HC     0.14000     4
>    CE2     C    -0.14000     5
>    HE2    HC     0.14000     5
>     CZ     C     0.20300     6
>     OH    OA    -0.61100     6
>     HH     H     0.40800     6
>      C     C       0.450     7
>      O     O      -0.450     7
> ---------------------------------------
> What is the difference with my case and these cases?
>

TYR is a single tyrosine residue.  The right-hand column is the charge group 
number.  Refer to the manual for the format.  All .rtp entries are single 
residues, by definition.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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