[gmx-users] atom labeling in forcefield file and pdbaredifferent

[Sanchaita Rajkhowa]

Hii, Thank you Justin for the help. I could successfully rename the atoms.
The crystal structure of my protein does not have any hydrogens in it but
still it is showing missing hydrogen atoms. I tried using -ignh command
but still can't fix this. Please help.

WARNING: atom AH61 is missing in residue NADH 301 in the pdb file


WARNING: atom AH62 is missing in residue NADH 301 in the pdb file


WARNING: atom AH2* is missing in residue NADH 301 in the pdb file


WARNING: atom AH3* is missing in residue NADH 301 in the pdb file


WARNING: atom NH71 is missing in residue NADH 301 in the pdb file


WARNING: atom NH72 is missing in residue NADH 301 in the pdb file


WARNING: atom NH2* is missing in residue NADH 301 in the pdb file


WARNING: atom NH3* is missing in residue NADH 301 in the pdb file


Fatal error:
There were 8 missing atoms in molecule Other, if you want to use this
incomplete topology anyhow, use the option -missing


What should I do??

>
>
> On 4/6/14, 10:29 AM, Sanchaita Rajkhowa wrote:
>>
>> 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?
>>
>
> The N prefix indicates atoms belonging to the nicotinamide nucleotide, A
> is for
> adenosine.
>
>> 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
>
> You will have to visualize the structure to determine what A and B
> represent
> (either adenosine or nicotinamide), then map that back to the NADH
> nomenclature
> in the force field.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA 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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-- 
SANCHAITA RAJKHOWA,
Research Scholar,
C/O Prof. Ramesh C. Deka,
Department of Chemical Science,
Tezpur University,
Napaam,
Tezpur-784 028


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