[gmx-users] Charmm36 in Gromacs: missing dihedrals
Jon Fuller
jonathan.fuller at gmail.com
Wed May 25 13:56:29 CEST 2011
Dear all,
I thought that I would reply to this thread as I am having similar
problems and there didn't seem to be an obvious solution.
I wanted to run a simulation of a POPE bilayer using the Charmm36
parameters from the Gromacs website. So I used pdb2gmx to generate a
.top file.
I used the input file from this website:
wget http://terpconnect.umd.edu/~jbklauda/research/download/pope80-c36npt.pdb
pdb2gmx -f pope80-c36npt.pdb -o pope.pdb -p pope.top -ff charmm36
(I then selected option 3 (tips3p charmm water))
I found that whilst pdb2gmx completes 'successfully', no bond, angle
or dihedral terms are generated in the resulting top file. I found
this behaviour when running both pdb2gmx version 4.5.3 and version
4.5.4. As a further check I also found the same behaviour if I used
the charmm27 parameters. I found this related thread, but there was no
obvious solution to the problem.
As far as I can tell I am using a reasonable procedure. Can anyone
spot something that I'm doing wrong to cause this behaviour?
I have pasted the output from pdb2gmx below and truncated results from
the top file below this.
Many thanks in advance,
Jon
:-) G R O M A C S (-:
GROningen Mixture of Alchemy and Childrens' Stories
:-) VERSION 4.5.3 (-:
...
...
Using the Charmm36 force field in directory charmm36.ff
Opening force field file
/home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/watermodels.dat
Select the Water Model:
1: TIP3P TIP 3-point, recommended
2: TIP4P TIP 4-point
3: TIPS3P CHARMM TIP 3-point with LJ on H's (note: twice as slow in GROMACS)
4: SPC simple point charge
5: SPC/E extended simple point charge
6: None
3
Opening force field file
/home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/aminoacids.r2b
Reading pope80-c36npt.pdb...
Read 17683 atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
There are 1 chains and 0 blocks of water and 256 residues with 17683 atoms
chain #res #atoms
1 ' ' 2641 17683
All occupancies are one
Opening force field file
/home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/atomtypes.atp
Atomtype 1
Reading residue database... (charmm36)
Opening force field file
/home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/aminoacids.rtp
Residue 41
Sorting it all out...
Opening force field file
/home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/dna.rtp
Residue 53
Sorting it all out...
Opening force field file
/home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/lipids.rtp
Residue 89
Sorting it all out...
Opening force field file
/home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/rna.rtp
Residue 101
Sorting it all out...
Opening force field file
/home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/aminoacids.hdb
Opening force field file
/home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/lipids.hdb
Opening force field file
/home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/aminoacids.n.tdb
Opening force field file
/home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/aminoacids.c.tdb
Processing chain 1 (17683 atoms, 2641 residues)
There are 80 donors and 0 acceptors
There are 0 hydrogen bonds
Warning: Starting residue POPE1 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue POPE2 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue POPE3 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue POPE4 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue POPE5 in chain not identified as Protein/RNA/DNA.
More than 5 unidentified residues at start of chain - disabling
further warnings.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file
/home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/aminoacids.arn
Checking for duplicate atoms....
Now there are 2641 residues with 17683 atoms
Making bonds...
Number of bonds was 17603, now 17603
Generating angles, dihedrals and pairs...
Before cleaning: 26320 pairs
Before cleaning: 26320 dihedrals
Keeping all generated dihedrals
Making cmap torsions...There are 26320 dihedrals, 160 impropers, 26723 angles
26320 pairs, 17603 bonds and 0 virtual sites
Total mass 103578.495 a.m.u.
Total charge 0.000 e
Writing topology
Writing coordinate file...
--------- PLEASE NOTE ------------
You have successfully generated a topology from: pope80-c36npt.pdb.
The Charmm36 force field and the tips3p water model are used.
--------- ETON ESAELP ------------
###
# pope.top
###
;
; File 'pope.top' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Mon May 23 17:31:33 2011
;
; This is a standalone topology file
;
; It was generated using program:
; pdb2gmx - VERSION 4.5.3
;
; Command line was:
; pdb2gmx -f pope80-c36npt.pdb -o pope.pdb -p pope.top -ff charmm36
;
; Force field was read from the standard Gromacs share directory.
;
; Include forcefield parameters
#include "charmm36.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Other 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
; residue 1 POPE rtp POPE q 0.0
1 NH3L 1 POPE N 1 -0.3 14.007
; qtot -0.3
2 HCL 1 POPE HN1 2 0.33 1.008
; qtot 0.03
3 HCL 1 POPE HN2 3 0.33 1.008
; qtot 0.36
4 HCL 1 POPE HN3 4 0.33 1.008
; qtot 0.69
5 CTL2 1 POPE C12 5 0.13 12.011
; qtot 0.82
6 HAL2 1 POPE H12A 6 0.09 1.008
; qtot 0.91
7 HAL2 1 POPE H12B 7 0.09 1.008 ; qtot 1
8 CTL2 1 POPE C11 8 -0.08 12.011
; qtot 0.92
9 HAL2 1 POPE H11A 9 0.09 1.008
; qtot 1.01
10 HAL2 1 POPE H11B 10 0.09 1.008 ; qtot 1.1
11 PL 1 POPE P 11 1.5 30.974 ; qtot 2.6
12 O2L 1 POPE O13 12 -0.78 15.9994
; qtot 1.82
13 O2L 1 POPE O14 13 -0.78 15.9994
; qtot 1.04
14 OSLP 1 POPE O11 14 -0.57 15.9994
; qtot 0.47
15 OSLP 1 POPE O12 15 -0.57 15.9994
; qtot -0.1
16 CTL2 1 POPE C1 16 -0.08 12.011
; qtot -0.18
17 HAL2 1 POPE HA 17 0.09 1.008
; qtot -0.09
18 HAL2 1 POPE HB 18 0.09 1.008 ; qtot 0
19 CTL1 1 POPE C2 19 0.17 12.011
; qtot 0.17
20 HAL1 1 POPE HS 20 0.09 1.008
; qtot 0.26
21 OSL 1 POPE O21 21 -0.49 15.9994
; qtot -0.23
22 CL 1 POPE C21 22 0.9 12.011
; qtot 0.67
23 OBL 1 POPE O22 23 -0.63 15.9994
; qtot 0.04
24 CTL2 1 POPE C22 24 -0.22 12.011
; qtot -0.18
25 HAL2 1 POPE H2R 25 0.09 1.008
; qtot -0.09
26 HAL2 1 POPE H2S 26 0.09 1.008 ; qtot 0
27 CTL2 1 POPE C3 27 0.08 12.011
; qtot 0.08
28 HAL2 1 POPE HX 28 0.09 1.008
; qtot 0.17
29 HAL2 1 POPE HY 29 0.09 1.008
; qtot 0.26
30 OSL 1 POPE O31 30 -0.49 15.9994
; qtot -0.23
31 CL 1 POPE C31 31 0.9 12.011
; qtot 0.67
32 OBL 1 POPE O32 32 -0.63 15.9994
; qtot 0.04
33 CTL2 1 POPE C32 33 -0.22 12.011
; qtot -0.18
34 HAL2 1 POPE H2X 34 0.09 1.008
; qtot -0.09
35 HAL2 1 POPE H2Y 35 0.09 1.008 ; qtot 0
36 CTL2 1 POPE C23 36 -0.18 12.011
; qtot -0.18
37 HAL2 1 POPE H3R 37 0.09 1.008
; qtot -0.09
38 HAL2 1 POPE H3S 38 0.09 1.008 ; qtot 0
39 CTL2 1 POPE C24 39 -0.18 12.011
; qtot -0.18
40 HAL2 1 POPE H4R 40 0.09 1.008
; qtot -0.09
41 HAL2 1 POPE H4S 41 0.09 1.008 ; qtot 0
42 CTL2 1 POPE C25 42 -0.18 12.011
; qtot -0.18
43 HAL2 1 POPE H5R 43 0.09 1.008
; qtot -0.09
44 HAL2 1 POPE H5S 44 0.09 1.008 ; qtot 0
45 CTL2 1 POPE C26 45 -0.18 12.011
; qtot -0.18
46 HAL2 1 POPE H6R 46 0.09 1.008
; qtot -0.09
47 HAL2 1 POPE H6S 47 0.09 1.008 ; qtot 0
48 CTL2 1 POPE C27 48 -0.18 12.011
; qtot -0.18
49 HAL2 1 POPE H7R 49 0.09 1.008
; qtot -0.09
50 HAL2 1 POPE H7S 50 0.09 1.008 ; qtot 0
51 CTL2 1 POPE C28 51 -0.18 12.011
; qtot -0.18
52 HAL2 1 POPE H8R 52 0.09 1.008
; qtot -0.09
53 HAL2 1 POPE H8S 53 0.09 1.008 ; qtot 0
54 CEL1 1 POPE C29 54 -0.15 12.011
; qtot -0.15
55 HEL1 1 POPE H91 55 0.15 1.008 ; qtot 0
56 CEL1 1 POPE C210 56 -0.15 12.011
; qtot -0.15
57 HEL1 1 POPE H101 57 0.15 1.008 ; qtot 0
58 CTL2 1 POPE C211 58 -0.18 12.011
; qtot -0.18
59 HAL2 1 POPE H11R 59 0.09 1.008
; qtot -0.09
60 HAL2 1 POPE H11S 60 0.09 1.008 ; qtot 0
61 CTL2 1 POPE C212 61 -0.18 12.011
; qtot -0.18
62 HAL2 1 POPE H12R 62 0.09 1.008
; qtot -0.09
63 HAL2 1 POPE H12S 63 0.09 1.008 ; qtot 0
64 CTL2 1 POPE C213 64 -0.18 12.011
; qtot -0.18
65 HAL2 1 POPE H13R 65 0.09 1.008
; qtot -0.09
66 HAL2 1 POPE H13S 66 0.09 1.008 ; qtot 0
67 CTL2 1 POPE C214 67 -0.18 12.011
; qtot -0.18
68 HAL2 1 POPE H14R 68 0.09 1.008
; qtot -0.09
69 HAL2 1 POPE H14S 69 0.09 1.008 ; qtot 0
70 CTL2 1 POPE C215 70 -0.18 12.011
; qtot -0.18
71 HAL2 1 POPE H15R 71 0.09 1.008
; qtot -0.09
72 HAL2 1 POPE H15S 72 0.09 1.008 ; qtot 0
73 CTL2 1 POPE C216 73 -0.18 12.011
; qtot -0.18
74 HAL2 1 POPE H16R 74 0.09 1.008
; qtot -0.09
75 HAL2 1 POPE H16S 75 0.09 1.008 ; qtot 0
76 CTL2 1 POPE C217 76 -0.18 12.011
; qtot -0.18
77 HAL2 1 POPE H17R 77 0.09 1.008
; qtot -0.09
78 HAL2 1 POPE H17S 78 0.09 1.008 ; qtot 0
79 CTL3 1 POPE C218 79 -0.27 12.011
; qtot -0.27
80 HAL3 1 POPE H18R 80 0.09 1.008
; qtot -0.18
81 HAL3 1 POPE H18S 81 0.09 1.008
; qtot -0.09
82 HAL3 1 POPE H18T 82 0.09 1.008 ; qtot 0
83 CTL2 1 POPE C33 83 -0.18 12.011
; qtot -0.18
84 HAL2 1 POPE H3X 84 0.09 1.008
; qtot -0.09
85 HAL2 1 POPE H3Y 85 0.09 1.008 ; qtot 0
86 CTL2 1 POPE C34 86 -0.18 12.011
; qtot -0.18
87 HAL2 1 POPE H4X 87 0.09 1.008
; qtot -0.09
88 HAL2 1 POPE H4Y 88 0.09 1.008 ; qtot 0
89 CTL2 1 POPE C35 89 -0.18 12.011
; qtot -0.18
90 HAL2 1 POPE H5X 90 0.09 1.008
; qtot -0.09
91 HAL2 1 POPE H5Y 91 0.09 1.008 ; qtot 0
92 CTL2 1 POPE C36 92 -0.18 12.011
; qtot -0.18
93 HAL2 1 POPE H6X 93 0.09 1.008
; qtot -0.09
94 HAL2 1 POPE H6Y 94 0.09 1.008 ; qtot 0
95 CTL2 1 POPE C37 95 -0.18 12.011
; qtot -0.18
96 HAL2 1 POPE H7X 96 0.09 1.008
; qtot -0.09
97 HAL2 1 POPE H7Y 97 0.09 1.008 ; qtot 0
98 CTL2 1 POPE C38 98 -0.18 12.011
; qtot -0.18
99 HAL2 1 POPE H8X 99 0.09 1.008
; qtot -0.09
100 HAL2 1 POPE H8Y 100 0.09 1.008 ; qtot 0
101 CTL2 1 POPE C39 101 -0.18 12.011
; qtot -0.18
102 HAL2 1 POPE H9X 102 0.09 1.008
; qtot -0.09
103 HAL2 1 POPE H9Y 103 0.09 1.008 ; qtot 0
104 CTL2 1 POPE C310 104 -0.18 12.011
; qtot -0.18
105 HAL2 1 POPE H10X 105 0.09 1.008
; qtot -0.09
106 HAL2 1 POPE H10Y 106 0.09 1.008 ; qtot 0
107 CTL2 1 POPE C311 107 -0.18 12.011
; qtot -0.18
108 HAL2 1 POPE H11X 108 0.09 1.008
; qtot -0.09
109 HAL2 1 POPE H11Y 109 0.09 1.008 ; qtot 0
110 CTL2 1 POPE C312 110 -0.18 12.011
; qtot -0.18
111 HAL2 1 POPE H12X 111 0.09 1.008
; qtot -0.09
112 HAL2 1 POPE H12Y 112 0.09 1.008 ; qtot 0
113 CTL2 1 POPE C313 113 -0.18 12.011
; qtot -0.18
114 HAL2 1 POPE H13X 114 0.09 1.008
; qtot -0.09
115 HAL2 1 POPE H13Y 115 0.09 1.008 ; qtot 0
116 CTL2 1 POPE C314 116 -0.18 12.011
; qtot -0.18
117 HAL2 1 POPE H14X 117 0.09 1.008
; qtot -0.09
118 HAL2 1 POPE H14Y 118 0.09 1.008 ; qtot 0
119 CTL2 1 POPE C315 119 -0.18 12.011
; qtot -0.18
120 HAL2 1 POPE H15X 120 0.09 1.008
; qtot -0.09
121 HAL2 1 POPE H15Y 121 0.09 1.008 ; qtot 0
122 CTL3 1 POPE C316 122 -0.27 12.011
; qtot -0.27
123 HAL3 1 POPE H16X 123 0.09 1.008
; qtot -0.18
124 HAL3 1 POPE H16Y 124 0.09 1.008
; qtot -0.09
125 HAL3 1 POPE H16Z 125 0.09 1.008 ; qtot 0
; residue 2 POPE rtp POPE q 0.0
126 NH3L 2 POPE N 126 -0.3 14.007
; qtot -0.3
127 HCL 2 POPE HN1 127 0.33 1.008
; qtot 0.03
128 HCL 2 POPE HN2 128 0.33 1.008
; qtot 0.36
129 HCL 2 POPE HN3 129 0.33 1.008
; qtot 0.69
...
; residue 256 TIP3 rtp TIP3 q 0.0
17678 OT 2560 TIP3 OH2 12560 -0.834 15.9994
; qtot -0.834
17679 HT 2560 TIP3 H1 12560 0.417 1.008
; qtot -0.417
17680 HT 2560 TIP3 H2 12560 0.417 1.008 ; qtot 0
...
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
1 5 1
5 6 1
5 7 1
....
9995 9999 1
9995 10000 1
9996 9998 1
9996 9999 1
9996 10000 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 5
2 1 4 5
2 1 5 5
3 1 4 5
3 1 5 5
4 1 5 5
....
17678 17679 17680 5
17678 17680 17679 5
17682 17681 17683 5
17681 17682 17683 5
17681 17683 17682 5
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
2 1 5 6 9
2 1 5 7 9
2 1 5 8 9
3 1 5 6 9
3 1 5 7 9
3 1 5 8 9
4 1 5 6 9
4 1 5 7 9
4 1 5 8 9
1 5 8 9 9
....
9772 9771 9774 9773 2
9781 9780 9783 9782 2
9897 9896 9899 9898 2
9906 9905 9908 9907 2
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "charmm36.ff/tips3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "charmm36.ff/ions.itp"
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Other 1
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