[gmx-users] pdb2gmx & terminal residues
Justin Lemkul
jalemkul at vt.edu
Thu Mar 31 16:46:00 CEST 2016
On 3/31/16 10:41 AM, Brett wrote:
> Dear Justin and All,
>
> The full screen output was as following and I am looking forward to getting a reply from you.
>
>
>
>
> gmx pdb2gmx -f practice.pdb -o target_processed.gro -ignh
> :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-:
>
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> Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
> Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
> Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
> Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
> Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
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> check out http://www.gromacs.org for more information.
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>
> GROMACS: gmx pdb2gmx, VERSION 5.1.2
> Executable: /usr/local/gromacs/bin/gmx
> Data prefix: /usr/local/gromacs
> Command line:
> gmx pdb2gmx -f practice.pdb -o target_processed.gro -ignh
>
>
> Select the Force Field:
> From '/usr/local/gromacs/share/gromacs/top':
> 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
> 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
> 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
> 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
> 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
> 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
> 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
> 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
> 9: GROMOS96 43a1 force field
> 10: GROMOS96 43a2 force field (improved alkane dihedrals)
> 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> 14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
> 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 14
>
> Using the Gromos54a7 force field in directory gromos54a7.ff
>
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/watermodels.dat
>
> Select the Water Model:
> 1: SPC simple point charge, recommended
> 2: SPC/E extended simple point charge
> 3: None
> 1
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.r2b
> Reading practice.pdb...
> Read 331 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 1 chains and 0 blocks of water and 42 residues with 331 atoms
>
> chain #res #atoms
> 1 'N' 42 331
>
> All occupancies are one
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/atomtypes.atp
> Atomtype 58
> Reading residue database... (gromos54a7)
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.rtp
> Using default: not generating all possible dihedrals
> Using default: excluding 3 bonded neighbors
> Using default: generating 1,4 H--H interactions
> Using default: removing proper dihedrals found on the same bond as a proper dihedral
> Residue 108
> Sorting it all out...
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.hdb
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb
> Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb
> Processing chain 1 'N' (331 atoms, 42 residues)
> Identified residue ASP288 as a starting terminus.
> Identified residue ILE329 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Start terminus ASP-288: NH3+
> End terminus ILE-329: COO-
> Checking for duplicate atoms....
> Now there are 330 atoms. Deleted 1 duplicates.
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 42 residues with 417 atoms
> Making bonds...
> Number of bonds was 424, now 419
> Generating angles, dihedrals and pairs...
>
> 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.
>
>
> Before cleaning: 711 pairs
> Before cleaning: 847 dihedrals
> Making cmap torsions...
> There are 313 dihedrals, 181 impropers, 608 angles
> 711 pairs, 419 bonds and 0 virtual sites
> Total mass 4704.396 a.m.u.
> Total charge -1.000 e
> Writing topology
>
> Writing coordinate file...
> --------- PLEASE NOTE ------------
> You have successfully generated a topology from: practice.pdb.
> The Gromos54a7 force field and the spc water model are used.
> --------- ETON ESAELP ------------
>
> gcq#564: "Even if you are on the right track, you will get run over if you just sit there." (Will Rogers)
> --------------------------------------
>
Those warnings shouldn't normally show up, but they aren't indicating a problem
because your topology is being written successfully.
-Justin
>
>
>
>
>
>
> At 2016-03-31 22:33:21, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>
>>
>> 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
>>>>
>>>> ==================================================
>>>> --
>>>> Gromacs Users mailing list
>>>>
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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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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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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