[gmx-users] pdb2gmx & terminal residues
Brett
brettliu123 at 163.com
Thu Mar 31 16:41:26 CEST 2016
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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Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
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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)
--------------------------------------
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!
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>
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