[gmx-users] Fix the residues
liming_52
liming_52 at 163.com
Fri Jan 6 20:57:27 CET 2017
Thank you for reppy. The full information is as follows:
$ gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water spce
:-) GROMACS - gmx pdb2gmx, VERSION 5.1.4 (-:
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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
Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
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GROMACS: gmx pdb2gmx, VERSION 5.1.4
Executable: /usr/local/gromacs/bin//gmx.exe
Data prefix: /usr/local/gromacs
Command line:
gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water spce
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)
9
Using the Gromos43a1 force field in directory gromos43a1.ff
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.r2b
Reading lactoferrin.pdb...
WARNING: all CONECT records are ignored
Read 2560 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 335 residues with 2560 atoms
chain #res #atoms
1 'A' 335 2560
All occupancies are one
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/atomtypes.atp
Atomtype 50
Reading residue database... (gromos43a1)
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.rtp
Residue 96
Sorting it all out...
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.1#
Processing chain 1 'A' (2560 atoms, 335 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 500 donors and 499 acceptors were found.
There are 743 hydrogen bonds
Will use HISE for residue 420
Will use HISH for residue 458
Will use HISD for residue 588
Will use HISE for residue 595
Will use HISE for residue 606
Will use HISE for residue 613
Identified residue TYR342 as a starting terminus.
Identified residue SER676 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS348 CYS358 CYS371 CYS380 CYS405 HIS420 CYS425
SG64 SG138 SG241 SG300 SG481 NE2595 SG629
CYS358 SG138 0.849
CYS371 SG241 0.940 0.213
CYS380 SG300 0.204 0.933 1.049
CYS405 SG481 1.411 2.186 2.303 1.371
HIS420 NE2595 3.406 3.321 3.509 3.348 3.338
CYS425 SG629 2.460 2.150 2.323 2.429 2.901 1.313
CYS457 SG875 2.702 2.932 3.096 2.502 2.930 3.532 3.094
HIS458 NE2885 2.548 2.968 3.141 2.345 2.426 3.418 3.123
MET471 SD983 2.682 3.182 3.361 2.487 2.293 3.347 3.207
CYS481 SG1051 3.086 3.770 3.933 2.924 2.167 3.844 3.883
CYS491 SG1133 2.184 2.509 2.651 1.985 2.495 3.728 3.130
CYS502 SG1209 2.159 2.671 2.793 1.969 2.249 4.093 3.530
CYS505 SG1228 2.166 2.539 2.672 1.970 2.452 3.880 3.273
CYS515 SG1297 2.029 2.503 2.628 1.837 2.216 3.962 3.362
CYS532 SG1436 2.629 2.850 3.005 2.431 2.930 3.653 3.146
CYS573 SG1764 3.775 3.952 4.158 3.598 3.597 2.648 2.951
CYS587 SG1867 3.594 3.755 3.960 3.419 3.463 2.533 2.771
HIS588 NE21877 3.277 3.459 3.671 3.127 3.007 1.800 2.233
HIS595 NE21927 1.637 1.836 2.046 1.488 1.825 2.179 1.605
HIS606 NE22008 1.686 1.478 1.480 1.846 2.316 3.172 2.230
HIS613 NE22066 2.250 1.623 1.635 2.359 3.154 2.929 1.780
CYS625 SG2156 2.333 1.651 1.753 2.329 3.350 2.606 1.332
CYS630 SG2197 2.270 1.572 1.667 2.261 3.342 2.763 1.491
CYS647 SG2337 2.306 2.002 2.173 2.286 2.760 1.421 0.205
CYS675 SG2554 2.907 3.577 3.743 2.742 2.024 3.670 3.679
CYS457 HIS458 MET471 CYS481 CYS491 CYS502 CYS505
SG875 NE2885 SD983 SG1051 SG1133 SG1209 SG1228
HIS458 NE2885 0.746
MET471 SD983 1.209 0.486
CYS481 SG1051 2.332 1.591 1.152
CYS491 SG1133 0.700 0.843 1.287 2.240
CYS502 SG1209 1.263 1.036 1.308 1.939 0.670
CYS505 SG1228 0.873 0.919 1.329 2.200 0.207 0.484
CYS515 SG1297 1.171 1.014 1.329 2.039 0.523 0.202 0.343
CYS532 SG1436 0.207 0.847 1.329 2.423 0.569 1.166 0.740
CYS573 SG1764 1.883 1.857 1.818 2.626 2.461 2.877 2.626
CYS587 SG1867 1.757 1.754 1.744 2.603 2.323 2.759 2.493
HIS588 NE21877 2.175 1.985 1.862 2.508 2.559 2.918 2.715
HIS595 NE21927 1.755 1.601 1.689 2.421 1.670 1.978 1.789
HIS606 NE22008 4.076 3.936 3.996 4.306 3.707 3.784 3.737
HIS613 NE22066 4.109 4.155 4.299 4.857 3.868 4.130 3.948
CYS625 SG2156 3.130 3.389 3.640 4.482 3.059 3.515 3.190
CYS630 SG2197 3.034 3.320 3.592 4.455 2.945 3.405 3.073
CYS647 SG2337 3.121 3.125 3.204 3.846 3.112 3.483 3.246
CYS675 SG2554 2.186 1.441 1.001 0.209 2.089 1.817 2.058
CYS515 CYS532 CYS573 CYS587 HIS588 HIS595 HIS606
SG1297 SG1436 SG1764 SG1867 NE21877 NE21927 NE22008
CYS532 SG1436 1.063
CYS573 SG1764 2.816 2.085
CYS587 SG1867 2.687 1.956 0.205
HIS588 NE21877 2.835 2.354 0.952 0.859
HIS595 NE21927 1.831 1.805 2.198 2.012 1.663
HIS606 NE22008 3.645 4.043 4.641 4.457 3.901 2.523
HIS613 NE22066 3.956 4.078 4.559 4.364 3.878 2.644 1.163
CYS625 SG2156 3.318 3.104 3.598 3.398 3.138 2.074 2.269
CYS630 SG2197 3.206 2.996 3.606 3.404 3.187 2.069 2.325
CYS647 SG2337 3.316 3.165 3.060 2.878 2.325 1.567 2.028
CYS675 SG2554 1.902 2.278 2.507 2.470 2.354 2.213 4.124
HIS613 CYS625 CYS630 CYS647
NE22066 SG2156 SG2197 SG2337
CYS625 SG2156 1.454
CYS630 SG2197 1.554 0.210
CYS647 SG2337 1.628 1.318 1.473
CYS675 SG2554 4.656 4.273 4.247 3.642
Linking CYS-348 SG-64 and CYS-380 SG-300...
Linking CYS-358 SG-138 and CYS-371 SG-241...
Linking CYS-425 SG-629 and CYS-647 SG-2337...
Linking CYS-457 SG-875 and CYS-532 SG-1436...
Linking CYS-481 SG-1051 and CYS-675 SG-2554...
Linking CYS-491 SG-1133 and CYS-505 SG-1228...
Linking CYS-502 SG-1209 and CYS-515 SG-1297...
Linking CYS-573 SG-1764 and CYS-587 SG-1867...
Linking CYS-625 SG-2156 and CYS-630 SG-2197...
Start terminus TYR-342: NH3+
End terminus SER-676: COO-
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 335 residues with 3278 atoms
Making bonds...
Number of bonds was 3340, now 3335
Generating angles, dihedrals and pairs...
WARNING: WARNING: Residue 1 named TYR 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 335 named SER 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: 5477 pairs
Before cleaning: 6310 dihedrals
Making cmap torsions...
There are 1781 dihedrals, 1618 impropers, 4878 angles
5477 pairs, 3335 bonds and 0 virtual sites
Total mass 36559.344 a.m.u.
Total charge 0.000 e
Writing topology
Back Off! I just backed up posre.itp to ./#posre.itp.1#
Writing coordinate file...
Back Off! I just backed up lactoferrin.gro to ./#lactoferrin.gro.1#
--------- PLEASE NOTE ------------
You have successfully generated a topology from: lactoferrin.pdb.
The Gromos43a1 force field and the spce water model are used.
--------- ETON ESAELP ------------
gcq#395: "It was something to at least have a choice of nightmares" (Joseph Conrad)
--
With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China
At 2017-01-07 03:22:36, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>On 1/6/17 1:58 PM, liming_52 wrote:
>> Dear Gromacs users,
>>
>> I am trying to run a md using 4n6p.cif, which was obtained from PDB. I converted the file into pdb format using DS4.1, and got the file named lactoferrin.pdb. When I directly run
>> the command "gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water spce", the program runs and produces the information as follows:
>> ...
>
>You snipped out the most important information. Please provide the full screen
>output from pdb2gmx.
>
>-Justin
>
>> WARNING: WARNING: Residue 1 named TYR 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 335 named SER 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.
>>
>> ...
>> How should I fix the residues? And which tools should I use? Is there any examples or tutorials?
>>
>> If anyone can suggest a solution to this issue, it would be really helpful.
>>
>>
>>
>>
>>
>>
>>
>> --
>>
>> With my best wishes,
>> Ming Li, PhD
>> Chinese Academy of Agricultural Sciences, Beijing, China
>>
>
>--
>==================================================
>
>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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