Hello. I will try now to send part of my itp file and if another part of the file is needed I will send it if requested. Below are the emails that were already sent regarding my problem. I hope I have not caused any incovenience. FabrÃcio Bracht
" I am working with a protein-ligand complex in gromacs with ffamber99 forcefield. I was able to generate the topology file for my ligand with acpypi. Was also able to insert the ligand coordinates into my protein's coordinate file. Was also able to generate the water box with genbox. The number of molecules all match, the ligand coordinates are still there but grompp tells me that: Fatal error: Found a second defaults directive, file "ligand.itp", line 5 I've checked wikigromacs, but the solution given there, to simply erase the second default line does not suit me here. Once I do this, i mean, go to my ligand.itp file and put a ; before my default section, grompp does not recognize anymore that my ligand is there and gives out another error line. I would like some advice on the matter if possible. Thank you in advance FabrÃcio Bracht >Well, it's not like grompp is recognizing you have a ligand there >right now, is it? grompp doesn't reach the point where it realizes you >don't seem to have a ligand. It seems there's something wrong with the >topology. Better post ligand.itp, like Justin suggests, and also give >the error which occurs when you do comment out the defaults line in >the ligand topology. > >Cheers, > >Tsjerk " Now, the actual itp file. ; M_E.top created by acpypi on Wed Nov 26 18:00:37 2008 [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb o o 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 c c 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 oh oh 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 ho ho 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000 c3 c3 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 hc hc 0.00000 0.00000 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157 c2 c2 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ha ha 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 ce ce 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 cf cf 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 [ moleculetype ] ;name nrexcl M_E 3 [ atoms ] ; nr type resi res atom cgnr charge mass typeB chargeB 1 o 1 M_E O49 1 -0.55230 16.00000 ; qtot -0.552 2 c 1 M_E C48 2 0.63200 12.01000 ; qtot 0.080 3 oh 1 M_E O50 3 -0.60900 16.00000 ; qtot -0.529 4 ho 1 M_E H51 4 0.44690 1.00800 ; qtot -0.082 5 c3 1 M_E C45 5 -0.12590 12.01000 ; qtot -0.208 6 hc 1 M_E H46 6 0.08080 1.00800 ; qtot -0.127 7 hc 1 M_E H47 7 0.08110 1.00800 ; qtot -0.046 8 c3 1 M_E C42 8 -0.07210 12.01000 ; qtot -0.118 9 hc 1 M_E H43 9 0.06640 1.00800 ; qtot -0.052 10 hc 1 M_E H44 10 0.05040 1.00800 ; qtot -0.002 11 c3 1 M_E C39 11 -0.05170 12.01000 ; qtot -0.053 12 hc 1 M_E H40 12 0.04490 1.00800 ; qtot -0.008 13 hc 1 M_E H41 13 0.05410 1.00800 ; qtot 0.046 14 c2 1 M_E C37 14 -0.16730 12.01000 ; qtot -0.122 15 ha 1 M_E H38 15 0.11950 1.00800 ; qtot -0.002 16 c2 1 M_E C35 16 -0.16710 12.01000 ; qtot -0.169 17 ha 1 M_E H36 17 0.11730 1.00800 ; qtot -0.052 18 c3 1 M_E C32 18 -0.04940 12.01000 ; qtot -0.101 19 hc 1 M_E H33 19 0.07250 1.00800 ; qtot -0.029 20 hc 1 M_E H34 20 0.06180 1.00800 ; qtot 0.033 21 c3 1 M_E C2 21 -0.00340 12.01000 ; qtot 0.030 22 hc 1 M_E H6 22 0.07250 1.00800 ; qtot 0.102 23 c2 1 M_E C1 23 -0.10390 12.01000 ; qtot -0.002 24 ha 1 M_E H8 24 0.14850 1.00800 ; qtot 0.147 25 ce 1 M_E C5 25 -0.25360 12.01000 ; qtot -0.107 26 ha 1 M_E H9 26 0.16130 1.00800 ; qtot 0.054 27 c 1 M_E C4 27 0.56070 12.01000 ; qtot 0.615 28 o 1 M_E O7 28 -0.52650 16.00000 ; qtot 0.089 29 ce 1 M_E C3 29 -0.21970 12.01000 ; qtot -0.131 30 cf 1 M_E C10 30 -0.04110 12.01000 ; qtot -0.172 31 ha 1 M_E H11 31 0.14510 1.00800 ; qtot -0.027 32 cf 1 M_E C12 32 -0.16880 12.01000 ; qtot -0.196 33 ha 1 M_E H13 33 0.12600 1.00800 ; qtot -0.070 34 c2 1 M_E C14 34 -0.12090 12.01000 ; qtot -0.191 35 ha 1 M_E H15 35 0.12220 1.00800 ; qtot -0.069 36 c3 1 M_E C16 36 -0.06070 12.01000 ; qtot -0.129 37 hc 1 M_E H17 37 0.05610 1.00800 ; qtot -0.073 38 hc 1 M_E H18 38 0.05520 1.00800 ; qtot -0.018 39 c3 1 M_E C19 39 -0.07610 12.01000 ; qtot -0.094 40 hc 1 M_E H20 40 0.04810 1.00800 ; qtot -0.046 41 hc 1 M_E H21 41 0.03740 1.00800 ; qtot -0.009 42 c3 1 M_E C22 42 -0.07850 12.01000 ; qtot -0.087 43 hc 1 M_E H23 43 0.04140 1.00800 ; qtot -0.046 44 hc 1 M_E H24 44 0.03920 1.00800 ; qtot -0.007 45 c3 1 M_E C25 45 -0.08090 12.01000 ; qtot -0.088 46 hc 1 M_E H26 46 0.03910 1.00800 ; qtot -0.048 47 hc 1 M_E H27 47 0.04220 1.00800 ; qtot -0.006 48 c3 1 M_E C28 48 -0.09280 12.01000 ; qtot -0.099 49 hc 1 M_E H29 49 0.03180 1.00800 ; qtot -0.067 50 hc 1 M_E H30 50 0.03440 1.00800 ; qtot -0.033 51 hc 1 M_E H31 51 0.03280 1.00800 ; qtot -0.000 [ bonds ] ; ai aj funct r k 3 4 1 9.7400e-02 3.0928e+05 ; O50 - H51 (more text not sent) [ pairs ] ; ai aj funct 6 9 1 ; H46 - H43 (more text not sent) [ angles ] ; ai aj ak funct theta cth 2 3 4 1 1.0737e+02 4.2844e+02 ; C48 - O50 - H51 (more text not sent) [ dihedrals ] ; propers ; treated as RBs in GROMACS to use combine multiple AMBER torsions per quartet ; i j k l func C0 C1 C2 C3 C4 C5 1 2 3 4 3 27.19600 -7.94960 -19.24640 0.00000 0.00000 0.00000 ; O49- C48- O50- H51 (more text not sent) [ dihedrals ] ; impropers ; treated as propers in GROMACS to use correct AMBER analytical function ; i j k l func phase kd pn 16 11 14 15 1 180.00 4.60240 2 ; C35- C39- C37- H38 (more text not sent) [ system ] M_E [ molecules ] ; Compound nmols M_E 1 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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