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 [EMAIL PROTECTED] 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 > > > -------------------------------- > > * > > * > * > ------------------------------------------------------------------------ > * > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php* _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
