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

[Justin Lemkul]

On 4/9/14, 8:01 AM, Sanchaita Rajkhowa wrote:
>
> 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??
>

If your input structure does not have all the required atoms, you need to make 
use of the .hdb file.  It appears that NADH is not present in any of them, so 
you will have to write the entry yourself.  Details of format are in the manual, 
and existing entries cover most, if not all, of the required functional groups.

-Justin

>>
>>
>> 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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>
>

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

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

==================================================