[gmx-users] The energy minimization....
Sampo Karkola
sampo.karkola at helsinki.fi
Thu Aug 16 10:39:57 CEST 2007
Hi,
I struggled with a similar minimisation problem with NADP (NDPP topology
in ffG43a1). Then I got a suggestion from a colleague in Prof. Ho"ltje's
group in Dusseldorf, that the atom naming should be changed from eg.
AC5* to something with only three characters, eg. C10. I renamed (and
only renamed) all the atoms with a unique running number and got rid of
the problem. I'm not sure if this will help you but it worked for me.
Hope it helps,
Sampo
mjduan at smail.hust.edu.cn wrote:
> http://www.gromacs.org/pipermail/gmx-users/2007-August/029155.html
>
>
>
> Mark:
> I am sorry to disturb you. I'm a beginner of GROMACS and this
> "mailing-list" system. I even don't know how to replay a post directly.
> And yesterday I haven't seen your replay because the list title changed,
> sorry again!
>
> About the problem, I haven't resolved it yet. The .top file of my ATP
> molecule is generated by the pdb2gmx, and the coordinates of each atom
> adopted to the pdb file. The force file is ffG43a2. Whether my topology
> file of ATP molecule have something wrong? The topology file of ATP as
> following:
>
> ; File '../ATP/ATP.top' was generated
> ; By user: root (0)
> ; On host: mjduan-desktop
> ; At date: Wed Aug 15 16:55:53 2007
> ;
> ; This is your topology file
> ; "Does All This Money Really Have To Go To Char ity ?" (Rick)
> ;
> ; Include forcefield parameters
> #include "ffG43a2.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> Protein 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 NR 1 ATP AN9 1 -0.2 14.0067 ;
> qtot -0.2
> 2 C 1 60; ATP AC4 1 0.2
> 12.011 ; qtot 0
> 3 NR 1 ATP AN3 2 -0.36 14.0067 ;
> qtot -0.36
> 4 CR1 1 ATP AC2 2 0.36 13.019 ;
> qtot 0
> 5 NR 1 ATP AN1 3 -0.36 14.0067 ;
> qtot -0.36
> 6 C 1 ATP AC6 3 0.36 12.011 ;
> qtot 0
> 7 NT 1 ATP AN6 4 -0.83 14.0067 ;
> qtot -0.83
> 8 H 1 ATP AH61 4 0.415 1.008 ;
> qtot -0.415
> 9 H 1&# 160; ATP AH62 4 0.415
> 1.008 ; qtot 0
> 10 C 1 ATP AC5 5 0 12.011 ;
> qtot 0
> 11 NR 1 ATP AN7 5 -0.36 14.0067 ;
> qtot -0.36
> 12 CR1 1 ATP AC8 5 0.36 13.019&#
> 160; ; qtot 0
> 13 CH1 1 ATP AC1* 6 0.2 13.019 ;
> qtot 0.2
> 14 OA 1 ATP AO4* 6 -0.36 15.9994 ;
> qtot -0.16
> 15 CH1 1 ATP AC4* 6 0.16 13.019 ;
> qtot 0
> 16 CH1 1 ATP AC2* & #160; 7 0.15
> 13.019 ; qtot 0.15
> 17 OA 1 ATP AO2* 7 -0.548 15.9994 ;
> qtot -0.398
> 18 H 1 ATP AH2* 7 0.398 1.008 ;
> qtot 0
> 19 CH1 1 ATP AC3* 8 0.15 13.019 ;
> qtot 0.15
> 20 &# 160; OA 1 ATP AO3* 8 -0.548
> 15.9994 ; qtot -0.398
> 21 H 1 ATP AH3* 8 0.398 1.008 ;
> qtot 0
> 22 CH2 1 ATP AC5* 9 0 14.027 ;
> qtot 0
> 23 OA 1 ATP AO5* 10 -0.36 60;
> 15.9994 ; qtot -0.36
> 24 P 1 ATP APA 10 0.705 30.9738 ;
> qtot 0.345
> 25 OM 1 ATP O1PA 10 -0.635 15.9994 ;
> qtot -0.29
> 26 OM 1 ATP O2PA 10 -0.635 15.9994 ;
> qtot -0.925
> 27 OA 1 ATP O3PA &# 160; 11 -0.36
> 15.9994 ; qtot -1.285
> 28 P 1 ATP APB 11 0.705 30.9738 ;
> qtot -0.58
> 29 OM 1 ATP O1PB 11 -0.635 15.9994 ;
> qtot -1.215
> 30 OM 1 ATP O2PB 11 -0.635 15.9994 ;
> qtot -1.85
> 31 OA &# 160; 1 ATP O3PB 12 -0.36
> 15.9994 ; qtot -2.21
> 32 P 1 ATP APG 12 0.63 30.9738 ;
> qtot -1.58
> 33 OM 1 ATP O1PG 12 -0.635 15.9994 ;
> qtot -2.215
> 34 OM 1 ATP O2PG 12 -0.635 15.9994 ;
> qtot -2.85
> ; 35 OA 1 ATP O3PG 12 -0.548 15.9994
> ; qtot -3.398
> 36 H 1 ATP H3PG 12 0.398 1.008 ;
> qtot -3
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 2 gb_9
> 1 ; 12 2 gb_9
> 1 13 2 gb_21
> 2 3 2 gb_11
> 2 10 2 gb_15
> 3 4 2 gb_6
> 4 5 2 gb_6
> 5 6 2 gb_11
> 6 7 2 gb_8
> 6 10 2 gb_15
> 7 8 2 gb_2
> 7 ; 9 2 gb_2
> 10 11 2 gb_9
> 11 12 2 gb_9
> 13 14 2 gb_19
> 13 16 2 gb_25
> 14 15 2 gb_19
> 15 19 2 gb_25
> 15 22 2 gb_25
> 16 17 2 gb_19
> 16 19 2 gb_25
> 17 18 2 gb_1* 19 20 2 gb_19
> 20 21 2 gb_1
> 22 23 2 gb_19
> 23 24 2 gb_27
> 24 25 2 gb_23
> 24 26 2 gb_23
> 24 27 2 gb_27
> 27 28 2 gb_27
> 28 29 2 gb_23
> 28 30 2 gb_23
> 28 31 2 0; gb_27
> 31 32 2 gb_27
> 32 33 2 gb_23
> 32 34 2 gb_23
> 32 35 2 gb_27
> 35 36 2 gb_1
>
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 1 15 1
> 1 17 1
> 0; 1 19 1
> 2 14 1
> 2 16 1
> 5 8 1
> 5 9 1
> 7 11 1
> 8 10 1
> 9 10 1
> 12 14 1
> 12 16 1
> 13 18 1
> 13 20 1
> 13 22 1
> 14 17 0; 1
> 14 20 1
> 14 23 1
> 15 17 1
> 15 21 1
> 15 24 1
> 16 21 1
> 16 22 1
> 17 20 1
> 18 19 1
> 19 23 1
> 20 22 1
> 22 25 1
> 22 26 1
> 22 27 1
> 23 28 1
> 24 29 1
> 24 30 1
> 24 31 1
> 25 28 1
> 26 28 1
> 27 32 1
> 28 33 1
> 28 34 1
> 28 35 1
> 29 32 1
> 30 32 1
>
> [ angles ]
> ; ai aj ak funct c0 c1
> c2 c3
> 2 1 12 2 ga_6
> 2 1 13 2 ga_36
> 12 1 13 2 ga_36
> 1 2 3 2 ga_38
> 1 2 10 2 ga_6
> 3 2 10 2 ga_26
> 2 3 4 2 ga_26
> 3 4 5 2 ga_26
> 4 5 6 2 ga_26
> 5 6 7 2 ga_26
> 5 6 10 2 ga_26
> 7 6 10 2 ga_26
> 6 7 8 2 ga_22
> 6 7 9 2 ga_22
> 8 & #160; 7 9 2 ga_23
> 2 10 6 2 ga_26
> 2 10 11 2 ga_6
> 6 10 11 2 ga_38
> 10 11 12 2 ga_6
> 1 12 11 2 ga_6
> 1 13 14 2 ga_8
> 1 13 16 2 ga_8
> 14 13 16 0; 2 ga_8
> 13 14 15 2 ga_9
> 14 15 19 2 ga_8
> 14 15 22 2 ga_8
> 19 15 22 2 ga_7
> 13 16 17 2 ga_8
> 13 16 19 2 ga_7
> 17 16 19 2 ga_8
> 16 17 18 2 ga_11
> 15 19 16&# 160; 2 ga_7
> 15 19 20 2 ga_8
> 16 19 20 2 ga_8
> 19 20 21 2 ga_11
> 15 22 23 2 ga_8
> 22 23 24 2 ga_25
> 23 24 25 2 ga_13
> 23 24 26 2 ga_13
> 23 24 27 2 ga_4
> 25 24 26 2 ga_28
> 25 24 27 2 ga_13
> 26 24 27 2 ga_13
> 24 27 28 2 ga_25
> 27 28 29 2 ga_13
> 27 28 30 2 ga_13
> 27 28 31 2 ga_4
> 29 28 30 2 ga_28
> 29 28 31 2 ga_13
> 60; 30 28 31 2 ga_13
> 28 31 32 2 ga_25
> 31 32 33 2 ga_13
> 31 32 34 2 ga_13
> 31 32 35 2 ga_4
> 33 32 34 2 ga_28
> 33 32 35 2 ga_13
> 34 32 35 2 ga_13
> 32 35 36 2 ga_11
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3 c4 c5
> 2 1 13 14 1 gd_6
> 10 6 7 8 1 gd_4
> 16 13 14 15 1 gd_14
> 1&# 160; 13 16 17 1 gd_7
> 14 13 16 17 1 gd_8
> 14 13 16 19 1 gd_17
> 14 13 16 19 1 gd_7
> 13 14 15 19 1 gd_14
> 14 15 19 16 1 gd_7
> 14 15 19 20 1 gd_8
> 22 15 19 0; 16 1 gd_17
> 22 15 19 20 1 gd_7
> 14 15 22 23 1 gd_8
> 19 15 22 23 1 gd_17
> 19 15 22 23 1 gd_7
> 13 16 17 18 1 gd_12
> 13 16 19 15 1 gd_17
> 13 16 19 20 1 gd_7
> 17 16 19 15 1 gd_7
> 17 16 19 20 1 gd_8
> 15 19 20 21 1 gd_12
> 15 22 23 24 1 gd_14
> 22 23 24 27 1 gd_11
> 22 23 24 27 1 gd_9
> 23 24 27 28 1 gd_11
> 23 24 27 28 1 gd_9
> 24 27 28 31 1 gd_11
> 24 27 28 31 1 gd_9
> 27 28 31 32 1 gd_11
> 27 28 31 32 1 gd_9
> 28 31 32 35 1 gd_11
> 28 31 32 35 1 gd_9
> 31 32 35 36 1 gd_11
> 31 32 35 36 1 gd_9
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3
> 1 12 11 10 2 gi_1
> 1 2 10 11 2 gi_1
> 1 12 2 13 2 gi_1
> 60; 2 3 4 5 2 gi_1
> 2 10 6 5 2 gi_1
> 2 1 3 10 2 gi_1
> 2 11 6 10 2 gi_1
> 2 1 12 11 2 gi_1
> 2 10 11 12 2 gi_1
> 3 2 10 6 2 gi_1
> 3 4 5 6 2 gi_1
> 4 3 2 10 2 gi_1
> 4 5 6 10 2 gi_1
> 6 9 8 7 2 gi_1
> 6 10 5 7 2 gi_1
> 10 2 1 12 2 gi_1
> 13 1 14 ; 16 2 gi_2
> 13 19 17 16 2 gi_2
> 15 14 22 19 2 gi_2
> 15 20 16 19 2 gi_2
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include water topology
> #include "spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 & #160; 1000 1000
> #endif
>
> ; Include generic topology for ions
> #include "ions.itp"
>
> [ system ]
> ; Name
> Protein in water
>
> [ molecules ]
> ; Compound #mols
> Protein 1
> SOL 871
>
>
> --------------------------------
>
> *
>
> *
> *
> ------------------------------------------------------------------------
> *
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