[gmx-users] pdb2gmx & terminal residues

[Brett]

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?

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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