[gmx-users] atom labeling in forcefield file and pdb aredifferent

[Sanchaita Rajkhowa]

Hii, I understand renaming the atoms in the coordinate file but how do I
do the one-to-one mapping of the atoms?? Which atom in the pdb file
represnt AP or AO5* in the forcefield file?

Atoms in gromos96 forcefield file-
[ NADH ]
 [ atoms ]
   AP     P     0.76000     0
 AO1P    OM    -0.63500     0
 AO2P    OM    -0.63500     0
 AO5*    OA    -0.36000     0
  O3P    OA    -0.26000     1
   NP     P     0.76000     1
 NO1P    OM    -0.63500     1
 NO2P    OM    -0.63500     1
 NO5*    OA    -0.36000     1
 AC5*   CH2     0.00000     2
 AC4*   CH1     0.16000     3
 AO4*    OA    -0.36000     3
 AC1*   CH1     0.20000     3
.
.
.

Atoms in pdb file-

  PA  NAD A 301      19.488  11.324  16.304  1.00 33.61           P
  O1A NAD A 301      20.484  12.030  15.464  1.00 34.53           O
  O2A NAD A 301      19.206  12.087  17.539  1.00 30.85           O
  O5B NAD A 301      19.972   9.804  16.571  1.00 32.18           O
  C5B NAD A 301      20.526   8.977  15.561  1.00 32.62           C
  C4B NAD A 301      21.503   7.982  16.198  1.00 31.90           C
  O4B NAD A 301      22.185   7.163  15.252  1.00 31.32           O
  C3B NAD A 301      22.594   8.724  16.954  1.00 31.17           C
  O3B NAD A 301      22.425   8.501  18.330  1.00 30.69           O
  C2B NAD A 301      23.888   8.185  16.376  1.00 30.92           C
  O2B NAD A 301      24.938   8.072  17.309  1.00 32.63           O
  C1B NAD A 301      23.424   6.848  15.845  1.00 30.98           C
  N9A NAD A 301      24.416   6.284  14.931  1.00 30.18           N
.
.
.

Thanks.

>
>
> On 4/4/14, 4:46 AM, Sanchaita wrote:
>> Hi, I am trying to perform the simulations of a particular protein
>> having
>> NADH as a cofactor.  However, when I try to run pdb2gmx command it
>> shows an error. It seems that the gromos96 43a2 force field has
>> parameters
>> for NADH but the labeling do not match the labeling done in the pdb
>> file.
>> What do I do? Please help.
>>
>
> Rename the atoms in the coordinate file to match the expectations of the
> .rtp file.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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> 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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-- 
SANCHAITA RAJKHOWA,
Research Scholar,
C/O Prof. Ramesh C. Deka,
Department of Chemical Science,
Tezpur University,
Napaam,
Tezpur-784 028


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