[gmx-users] pdb2gmx & terminal residues

Justin Lemkul jalemkul at vt.edu
Thu Mar 31 16:33:33 CEST 2016 


On 3/31/16 8:18 AM, Brett wrote:
> Dear Justin and All,
>
> For terminal residue, regardless I select 0, 1, 2, the error messages always exist.
>
> I have opened the pdb by swiss deep view and resaved it, the same error message still exist.
>
>
> However if I choose force field 6: AMBER99SB-ILDN protein, the error message disappear.
>
> Will you please give suggestions on getting rid of the warning messages for the terminal residues by pdb2gmx?
>

Please provide the full, unfiltered screen output from a functional and 
nonfunctional run through pdb2gmx.  There is no reason this shouldn't work out 
of the box.

-Justin

> Brett
>
>
>
>
>
>
>
>
>
> At 2016-03-31 19:12:38, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>
>>
>> On 3/30/16 10:41 PM, Brett wrote:
>>> Dear All,
>>>
>>> When I do "mx pdb2gmx -f practice.pdb -o target_processed.gro  -ignh" with force
>>> field, it gave me the warning as following,
>>>
>>> "WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was mapped
>>> to an entry in the topology database, but the atom H used in
>>> an interaction of type angle in that entry is not found in the
>>> input file. Perhaps your atom and/or residue naming needs to be
>>> fixed.
>>>
>>>
>>>
>>> WARNING: WARNING: Residue 42 named ILE of a molecule in the input file was mapped
>>> to an entry in the topology database, but the atom O used in
>>> an interaction of type angle in that entry is not found in the
>>> input file. Perhaps your atom and/or residue naming needs to be
>>> fixed.
>>> "
>>> I find Residue 1 (Asp) was exactly my N-terminal residue and Residue 42 was
>>> exactly my C-terminal residue.
>>>
>>> Here I copied the coordinates part for the N- and C-terminal residues here:
>>>
>>> ATOM  17737  N   ASP N 288     177.107 183.312 121.044  1.00500.00           N
>>> ATOM  17738  CA  ASP N 288     177.038 182.924 122.484  1.00500.00           C
>>> ATOM  17739  CB  ASP N 288     176.431 184.048 123.329  1.00500.00           C
>>> ATOM  17740  CG  ASP N 288     177.329 185.261 123.401  1.00500.00           C
>>> ATOM  17741  OD1 ASP N 288     178.383 185.181 124.068  1.00500.00           O
>>> ATOM  17742  OD2 ASP N 288     176.982 186.286 122.782  1.00500.00           O
>>> ATOM  17743  C   ASP N 288     176.265 181.626 122.691  1.00500.00           C
>>> ATOM  17744  O   ASP N 288     176.684 180.791 123.483  1.00500.00           O
>>> ATOM  17745  N   ARG N 289     175.144 181.458 121.984  1.00500.00           N
>>> (Residue 1 named ASP by GROMACS)
>>> .....
>>>
>>> ATOM  18058  O   SER N 328     177.424 180.662 130.523  1.00500.00           O
>>> ATOM  18059  N   ILE N 329     176.478 178.748 129.872  1.00500.00           N
>>> ATOM  18060  CA  ILE N 329     175.525 179.385 128.948  1.00500.00           C
>>> ATOM  18061  CB  ILE N 329     174.867 178.368 127.980  1.00499.43           C
>>> ATOM  18062  CG1 ILE N 329     175.920 177.731 127.065  1.00498.96           C
>>> ATOM  18063  CD1 ILE N 329     175.462 176.450 126.400  1.00498.79           C
>>> ATOM  18064  CG2 ILE N 329     173.789 179.040 127.126  1.00498.79           C
>>> ATOM  18065  C   ILE N 329     174.437 180.100 129.753  1.00498.62           C
>>> ATOM  18066  O   ILE N 329     173.671 179.471 130.483  1.00498.27           O
>>> ATOM  18067  O   ILE N 329     174.302 181.322 129.689  1.00496.91           O
>>> (Residue 42 named ILE  by GROMACS)
>>> TER
>>> END
>>>
>>> I myself cannot find anything wrong for my 2 terminal residues.
>>>
>>> Will you please take a look to see how to modify the 2 terminal residues so that
>>> the pdb2gmx will not give the warning messages?
>>>
>>> I am looking forward to getting a reply from you.
>>>
>>
>> The only way the above errors would show up is if you chose "None" for your
>> termini; choosing an appropriate NH3+/COO- will correct this. Note you have two
>> "O" in your C-terminal ILE, which is wrong as there should only be one, the
>> other should be OXT or whatever the force field wants (but again, the .tdb
>> patching mechanism takes care of this).
>>
>> -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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-- 
==================================================

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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