Hello guys:
I am building 11-cis-retinal topology these days. Here is what I did:
first of all, I build a small peptide like compound which
contains:11-cis-retinal connected to the protonated sidechain of LYS,
ACE and NME capped the N-term and C-term of the LYS respectively. With
this compound, I upload to paramchem and obtained a ligand.str file.
Second, I merged the information (including BONDS, ANGLES and DIHEDRALS)
of the ligand.str file into related section in par_all36_cgenff.prm.
Then I run charmm2gromacs-pvm.py with command:
python charmm2gromacs-pvm.py par_all36_cgenff.prm top_all36_cgenff.rtf
it generate a folder called cgenff-2b7.ff which includes the following
files:
aminoacids.rtp ffbonded.itp forcefield.doc
atomtypes.atp ffnonbonded.itp forcefield.itp
I merged the content of above files into gromacs CHARMM36.ff and build a
topology for 11-cis-retinal into aminoacids.rtp as following. This
toplogy only contains informations for 11-cis-retinal and protonated LYS:
-------------------------
[ RETK ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.18 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CG CT2 -0.18 7
HG1 HA 0.09 8
HG2 HA 0.09 9
CD CT2 -0.18 10
HD1 HA 0.09 11
HD2 HA 0.09 12
CE CT2 0.21 13
HE1 HA 0.05 14
HE2 HA 0.05 15
NZ NH3 -0.832 16
HZ1 HC 0.42 17
HZ2 HC 0.42 18
C C 0.51 20
O O -0.51 21
C1 CG301 0.000 22
C2 CG321 -0.182 23
C3 CG321 -0.177 24
C4 CG321 -0.183 25
C5 CG2DC1 -0.001 26
C6 CG2DC1 -0.001 27
C7 CG2DC2 -0.149 28
C8 CG2DC2 -0.150 29
C9 CG2DC1 -0.003 30
C10 CG2DC1 -0.134 31
C11 CG321 -0.190 32
C12 CG321 -0.187 33
C13 CG2D1 -0.005 34
C14 CG2D1 -0.043 35
C15 CG324 0.299 36
C16 CG331 -0.269 37
C17 CG331 -0.269 38
C18 CG331 -0.268 39
C19 CG331 -0.269 40
C20 CG331 -0.267 41
H7 HGA4 0.150 42
H8 HGA4 0.150 43
H10 HGA4 0.150 44
H14 HGA4 0.150 45
H21 HGA2 0.090 46
H22 HGA2 0.090 47
H31 HGA2 0.090 48
H32 HGA2 0.090 49
H41 HGA2 0.090 50
H42 HGA2 0.090 51
H111 HGA2 0.090 52
H112 HGA2 0.090 53
H121 HGA2 0.090 54
H122 HGA2 0.090 55
H151 HGA2 0.090 56
H152 HGA2 0.090 57
H161 HGA3 0.090 58
H162 HGA3 0.090 59
H163 HGA3 0.090 60
H171 HGA3 0.090 61
H172 HGA3 0.090 62
H173 HGA3 0.090 63
H181 HGA3 0.090 64
H182 HGA3 0.090 65
H183 HGA3 0.090 66
H191 HGA3 0.090 67
H192 HGA3 0.090 68
H193 HGA3 0.090 69
H201 HGA3 0.090 70
H202 HGA3 0.090 71
H203 HGA3 0.090 72
[ bonds ]
CB CA
CG CB
CD CG
CE CD
NZ CE
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
CG HG1
CG HG2
CD HD1
CD HD2
CE HE1
CE HE2
O C
NZ HZ1
NZ HZ2
NZ C15
C1 C2
C1 C6
C1 C16
C1 C17
C2 C3
C2 H21
C2 H22
C3 C4
C3 H31
C3 H32
C4 C5
C4 H41
C4 H42
C5 C6
C5 C18
C6 C7
C7 C8
C7 H7
C8 C9
C8 H8
C9 C10
C9 C19
C10 C11
C10 H10
C11 C12
C11 H111
C11 H112
C12 C13
C12 H121
C12 H122
C13 C14
C13 C20
C14 C15
C14 H14
C15 H151
C15 H152
C16 H161
C16 H162
C16 H163
C17 H171
C17 H172
C17 H173
C18 H181
C18 H182
C18 H183
C19 H191
C19 H192
C19 H193
C20 H201
C20 H202
C20 H203
[ impropers ]
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
-------------------------
with the new forcefild, I run pdb2gmx:
-------------------------
pdb2gmx -f input.pdb -o gmx.pdb
-------------------------
it finished without any warnings or errors for this step. However, when
I try to run grompp with command:
-------------------------
grompp_mpi -f em.mdp -c gmx.pdb -p topol.top
-------------------------
it failed with messages:
-------------------------
Program grompp_mpi, VERSION 4.6.2
Source code file:
/home/albert/Desktop/gromacs-4.6.2/src/kernel/topdirs.c, line: 106
Fatal error:
Invalid angle type 0
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------
Does anybody have any idea what's happening?
thank you very much.
Albert
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