[gmx-users] 11-cis retinal topology problem
Mark Abraham
mark.j.abraham at gmail.com
Sat Jul 6 11:10:16 CEST 2013
Not directly. grompp does have the ability to pinpoint the current
line, but nobody has extended that to this part of the code. You can
hack in some crude output to src/kernel/topio.c and recompile if you
want some clues where the issue arises. Change line 647 of that file
to add the second line below. Then recompile and run. You should be
able to just run grompp from your-cmake-build-dir/src/kernel/grompp
(i.e. no need to install modified code). The last line it mentions
should be where the problem exists.
set_warning_line(wi, cpp_cur_file(&handle),
cpp_cur_linenr(&handle));
warning_note(wi, "Debugging)";
Mark
On Sat, Jul 6, 2013 at 8:41 AM, Albert <mailmd2011 at gmail.com> wrote:
> 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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