[gmx-users] pdb2gmx disulfide bond formation - missing bond, angle, & dihedral types with all GROMOS FFs

Elizabeth Ploetz ploetz at ksu.edu
Wed Nov 23 00:32:28 CET 2011


Greetings Gromacs Users,

I am building the topology file for a protein with three disulfide bonds (bovine pancreatic trpysin inhibitor). When using any of the GROMOS FFs the topol.top output of pdb2gmx has missing bond, angle, and dihedral types on the lines describing the three disulfides. (The residue names do change appropriately i.e., CYS becomes CYS2.) The disulfides do form correctly when using the other currently available FFs. All the output shown below my message is from running GROMACS-4.5.5.  Note the same thing happens when running GROMACS-4.5.3 and GROMACS-4.0.5. 

I have not found any discussion of this issue on the internet (in general) or the gmx mailing list (specifically), however I suspect this may have contributed to at least one user message ( http://lists.gromacs.org/pipermail/gmx-users/2011-March/059242.html ). It is trivial to fill in the missing bond, angle, and dihedral types by hand after running pdb2gmx (this may be why this has not been discussed too much), but I am interested in figuring out a long term solution because the lab I work in has developed a FF which uses the GROMOS bonds and angles (and thus also uses the same format as GROMOS does for the ffbonded.itp file).  We hope to have our FF supported by GROMACS in the future, but we want to make sure that GROMACS users would not encounter this problem if they selected our FF.

Could anyone point me in the right direction?

Thanks for your consideration of this!

All the best,

Elizabeth A. Ploetz
Kansas State University

The list below shows the tested FFs. A '+' indicates proper disulfide description in the topology file, and an 'X' indicates the output contained missing bond/angle/dihedral types.  

Test of disulfide bond formation using pdb2gmx and FFs available in GROMACS-4.5.5:
+ 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 (with CMAP) - version 2.0
X 9: GROMOS96 43a1 force field
X10: GROMOS96 43a2 force field (improved alkane dihedrals)
X11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
X12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
X13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
+14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
+15: [DEPRECATED] Encad all-atom force field, using full solvent charges
+16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
+17: [DEPRECATED] Gromacs force field (see manual)
+18: [DEPRECATED] Gromacs force field with hydrogens for NMR  

This is an example of how I ran pdb2gmx:
                         :-)  G  R  O  M  A  C  S  (-:

                  Gromacs Runs On Most of All Computer Systems

                            :-)  VERSION 4.5.5  (-:
.
. skipping
.
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 (with CMAP) - version 2.0
 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: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
15: [DEPRECATED] Encad all-atom force field, using full solvent charges
16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
17: [DEPRECATED] Gromacs force field (see manual)
18: [DEPRECATED] Gromacs force field with hydrogens for NMR
13

Using the Gromos53a6 force field in directory gromos53a6.ff

Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.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/gromos53a6.ff/aminoacids.r2b
Reading ../start.pdb...
Read 'TRYPSIN INHIBITOR', 604 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 58 residues with 604 atoms

  chain  #res #atoms
  1 ' '    58    604  

All occupancies are one
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp
Atomtype 1
Reading residue database... (gromos53a6)
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.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 impropers on same bond as a proper
Residue 108
Sorting it all out...
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
Processing chain 1 (604 atoms, 58 residues)
Which LYSINE type do you want for residue 15
0. Not protonated (charge 0) (LYS)
1. Protonated (charge +1) (LYSH)

Type a number:1
Which LYSINE type do you want for residue 26
0. Not protonated (charge 0) (LYS)
1. Protonated (charge +1) (LYSH)
.
. skipping
. 
Type a number:0
Which GLUTAMIC ACID type do you want for residue 49
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUH)

Type a number:0
Identified residue ARG1 as a starting terminus.
Identified residue ALA58 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
                    CYS5   CYS14   CYS30   CYS38   CYS51   MET52
                    SG57   SG136   SG317   SG398   SG543   SD551
   CYS14   SG136   2.408
   CYS30   SG317   0.828   2.331
   CYS38   SG398   2.224   0.204   2.189
   CYS51   SG543   0.759   2.165   0.204   2.017
   MET52   SD551   0.928   2.703   0.373   2.560   0.550
   CYS55   SG585   0.204   2.316   0.664   2.137   0.573   0.805
Link CYS-5 SG-57 and CYS-55 SG-585 (y/n) ?y
Link CYS-14 SG-136 and CYS-38 SG-398 (y/n) ?y
Link CYS-30 SG-317 and CYS-51 SG-543 (y/n) ?y
Select start terminus type for ARG-1
 0: NH3+
 1: NH2
 2: None
0
Start terminus ARG-1: NH3+
Select end terminus type for ALA-58
 0: COO-
 1: COOH
 2: None
0
End terminus ALA-58: COO-
Checking for duplicate atoms....
Now there are 58 residues with 604 atoms
Making bonds...
Number of bonds was 623, now 618
Generating angles, dihedrals and pairs...
Before cleaning: 975 pairs
Before cleaning: 1187 dihedrals
Making cmap torsions...There are  329 dihedrals,  307 impropers,  906 angles
           975 pairs,      618 bonds and     0 virtual sites
Total mass 6517.563 a.m.u.
Total charge 6.000 e
Writing topology

Writing coordinate file...
		--------- PLEASE NOTE ------------
You have successfully generated a topology from: ../start.pdb.
The Gromos53a6 force field and the spc water model are used.
		--------- ETON ESAELP ------------

gcq#81: "Love is Like Moby Dick, Get Chewed and Get Spat Out" (Urban Dance Squad)


Here are the relevant sections of the output topology file when using GROMOS-53a6.
[ atoms ]
.
. skipping
.
; residue   5 CYS rtp CYS2 q  0.0
    53          N      5    CYS      N     21      -0.31    14.0067   ; qtot 0.69
    54          H      5    CYS      H     21       0.31      1.008   ; qtot 1
    55        CH1      5    CYS     CA     22          0     13.019   ; qtot 1
    56        CH2      5    CYS     CB     22          0     14.027   ; qtot 1
    57          S      5    CYS     SG     22          0      32.06   ; qtot 1
    58          C      5    CYS      C     23       0.45     12.011   ; qtot 1.45
    59          O      5    CYS      O     23      -0.45    15.9994   ; qtot 1
.
. skipping
.
; residue  14 CYS rtp CYS2 q  0.0
   132          N     14    CYS      N     60      -0.31    14.0067   ; qtot -0.31
   133          H     14    CYS      H     60       0.31      1.008   ; qtot 0
   134        CH1     14    CYS     CA     61          0     13.019   ; qtot 0
   135        CH2     14    CYS     CB     61          0     14.027   ; qtot 0
   136          S     14    CYS     SG     61          0      32.06   ; qtot 0
   137          C     14    CYS      C     62       0.45     12.011   ; qtot 0.45
   138          O     14    CYS      O     62      -0.45    15.9994   ; qtot 0
.
. skipping
.
; residue  30 CYS rtp CYS2 q  0.0
   313          N     30    CYS      N    133      -0.31    14.0067   ; qtot 3.69
   314          H     30    CYS      H    133       0.31      1.008   ; qtot 4
   315        CH1     30    CYS     CA    134          0     13.019   ; qtot 4
   316        CH2     30    CYS     CB    134          0     14.027   ; qtot 4
   317          S     30    CYS     SG    134          0      32.06   ; qtot 4
   318          C     30    CYS      C    135       0.45     12.011   ; qtot 4.45
   319          O     30    CYS      O    135      -0.45    15.9994   ; qtot 4
.
. skipping
.
; residue  38 CYS rtp CYS2 q  0.0
   394          N     38    CYS      N    170      -0.31    14.0067   ; qtot 3.69
   395          H     38    CYS      H    170       0.31      1.008   ; qtot 4
   396        CH1     38    CYS     CA    171          0     13.019   ; qtot 4
   397        CH2     38    CYS     CB    171          0     14.027   ; qtot 4
   398          S     38    CYS     SG    171          0      32.06   ; qtot 4
   399          C     38    CYS      C    172       0.45     12.011   ; qtot 4.45
   400          O     38    CYS      O    172      -0.45    15.9994   ; qtot 4
.
. skipping
.
; residue  51 CYS rtp CYS2 q  0.0
   539          N     51    CYS      N    225      -0.31    14.0067   ; qtot 5.69
   540          H     51    CYS      H    225       0.31      1.008   ; qtot 6
   541        CH1     51    CYS     CA    226          0     13.019   ; qtot 6
   542        CH2     51    CYS     CB    226          0     14.027   ; qtot 6
   543          S     51    CYS     SG    226          0      32.06   ; qtot 6
   544          C     51    CYS      C    227       0.45     12.011   ; qtot 6.45
   545          O     51    CYS      O    227      -0.45    15.9994   ; qtot 6.
.
. skipping
.
; residue  55 CYS rtp CYS2 q  0.0
   581          N     55    CYS      N    241      -0.31    14.0067   ; qtot 6.69
   582          H     55    CYS      H    241       0.31      1.008   ; qtot 7
   583        CH1     55    CYS     CA    242          0     13.019   ; qtot 7
   584        CH2     55    CYS     CB    242          0     14.027   ; qtot 7
   585          S     55    CYS     SG    242          0      32.06   ; qtot 7
   586          C     55    CYS      C    243       0.45     12.011   ; qtot 7.45
   587          O     55    CYS      O    243      -0.45    15.9994   ; qtot 7
.
. skipping
.
[ bonds ]
.
. skipping
.
   56    57     2    gb_32
   57   585     2
   58    59     2    gb_5
.
. skipping
.
  135   136     2    gb_32
  136   398     2
  137   138     2    gb_5
.
. skipping
.
  316   317     2    gb_32
  317   543     2
  318   319     2    gb_5
.
. skipping
.
[ angles ]
.
. skipping
.   
   55    56    57     2    ga_16
   56    57   585     2
   55    58    59     2    ga_30
.
. skipping
.
  134   135   136     2    ga_16
  135   136   398     2
  134   137   138     2    ga_30
.
. skipping
.
  315   316   317     2    ga_16
  316   317   543     2
  315   318   319     2    ga_30
.
. skipping
.
  396   397   398     2    ga_16
  136   398   397     2
  396   399   400     2    ga_30
.
. skipping
.
  541   542   543     2    ga_16
  317   543   542     2
  541   544   545     2    ga_30
.
. skipping
.
  583   584   585     2    ga_16
   57   585   584     2
  583   586   587     2    ga_30
.
. skipping
.
[ dihedrals ]
.
. skipping
.
   53    55    58    60     1    gd_40
   55    56    57   585     1
   56    57   585   584     1
   55    58    60    62     1    gd_14
.
. skipping
.
  132   134   137   139     1    gd_40
  134   135   136   398     1
  135   136   398   397     1
  134   137   139   141     1    gd_14
.
. skipping
.
  313   315   318   320     1    gd_40
  315   316   317   543     1
  316   317   543   542     1
  315   318   320   322     1    gd_14
.
. skipping
.
  394   396   399   401     1    gd_40
  396   397   398   136     1
  396   399   401   403     1    gd_14
.
. skipping
.
  539   541   544   546     1    gd_40
  541   542   543   317     1
  541   544   546   548     1    gd_14
.
. skipping
.
  581   583   586   588     1    gd_40
  583   584   585    57     1
  583   586   588   590     1    gd_14
.
. skipping
.


The GROMOS FFs all use a 'specbonds' section at the end of their ffbonded.itp files, which looks like this (below is an excerpt from gromos53a6.ff/ffbonded.itp):

; bond-, angle- and dihedraltypes for specbonds:
[ bondtypes ]
S      S       2    gb_36
NR     FE      2    gb_34

[ angletypes ]
CH1    CH2    S     2   ga_16
CH2    S      S     2   ga_6
CR1    NR    FE     2   ga_34
NR     FE    NR     2   ga_17

[ dihedraltypes ]
S      S      1   gd_21
NR     FE     1   gd_38
CH2    S      1   gd_26

while the other FFs do not use this method (as shown below).

Elizabeths-MacBook-Pro:top elizabethploetz$ pwd
/usr/local/gromacs/share/gromacs/top
Elizabeths-MacBook-Pro:top elizabethploetz$ grep 'specbond' */*
gromos43a1.ff/ffbonded.itp:; bond-, angle- and dihedraltypes for specbonds:
gromos43a2.ff/ffbonded.itp:; bond-, angle- and dihedraltypes for specbonds:
gromos45a3.ff/ffbonded.itp:; bond-, angle- and dihedraltypes for specbonds:
gromos53a5.ff/ffbonded.itp:; bond-, angle- and dihedraltypes for specbonds:
gromos53a6.ff/ffbonded.itp:; bond-, angle- and dihedraltypes for specbonds:

In a quick and dirty effort to mimic the other (working) FFs, I copied the /usr/local/gromacs/share/gromacs/top/gromos53a6.ff files into my local directory, commented out the 'specbonds' section of the ffbonded.itp file, and re-ran pdb2gmx using the local files.  This did not change the results however.



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