Dear GMX-Users I have a problem while trying to insert a drug molecule into my simulation. I have the topology file generated from the ATB-server. And accordingly I have edited the aminoacid.rtp & ffbonded.itp file. I have transcribed the forcefield parameters into GROMOS96 format. here is my .itp file for that molecule. My problem is that after doing all the things when i tried to do sd minimization then i got the error message like
*Program grompp, VERSION 4.5.5* *Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/topdirs.c, line: 107* * * *Fatal error:* *Invalid pairs type 180* *For more information and tips for troubleshooting, please check the GROMACS * *website at http://www.gromacs.org/Documentation/Errors* What may be the reason ? And when i studied through the .itp file then i have found the 1-4 interactions in the [ pairs ] section followed by the excluded 1-4 interactions. Now, my other question is that should I address these 1-4 interactions in the ffnonbonded.itp file ! Looking forward for kind response. [ moleculetype ] ; Name nrexcl _NW5 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass total_charge 1 CH3 1 _NW5 C14 1 -0.000 15.0350 ; 0.000 2 C 1 _NW5 C8 2 -0.217 12.0110 3 HC 1 _NW5 H1 2 0.138 1.0080 4 C 1 _NW5 C11 2 -0.111 12.0110 5 C 1 _NW5 C15 2 0.717 12.0110 6 O 1 _NW5 O1 2 -0.580 15.9994 7 N 1 _NW5 N2 2 -0.663 14.0067 8 H 1 _NW5 H8 2 0.372 1.0080 9 C 1 _NW5 C16 2 0.785 12.0110 10 NT 1 _NW5 N5 2 -0.939 14.0067 11 H 1 _NW5 H9 2 0.398 1.0080 12 H 1 _NW5 H10 2 0.398 1.0080 13 NR 1 _NW5 N1 2 -0.841 14.0067 14 H 1 _NW5 H7 2 0.347 1.0080 15 C 1 _NW5 C1 2 0.040 12.0110 16 C 1 _NW5 C2 2 0.040 12.0110 17 C 1 _NW5 C3 2 -0.151 12.0110 18 C 1 _NW5 C5 2 0.150 12.0110 19 C 1 _NW5 C13 2 0.149 12.0110 20 HC 1 _NW5 H14 2 0.099 1.0080 21 NR 1 _NW5 N3 2 -0.567 14.0067 22 NR 1 _NW5 N4 2 0.436 14.0067 ; 0.000 23 C 1 _NW5 C10 3 -0.154 12.0110 24 HC 1 _NW5 H6 3 0.154 1.0080 ; 0.000 25 C 1 _NW5 C6 4 -0.154 12.0110 26 HC 1 _NW5 H3 4 0.154 1.0080 ; 0.000 27 C 1 _NW5 C4 5 -0.154 12.0110 28 HC 1 _NW5 H2 5 0.154 1.0080 ; 0.000 29 C 1 _NW5 C9 6 -0.152 12.0110 30 HC 1 _NW5 H5 6 0.152 1.0080 ; 0.000 31 C 1 _NW5 C7 7 -0.154 12.0110 32 HC 1 _NW5 H4 7 0.154 1.0080 ; 0.000 33 C 1 _NW5 C12 8 -0.200 12.0110 34 HC 1 _NW5 H15 8 0.200 1.0080 ; 0.000 ; total charge of the molecule: 0.000 [ bonds ] ; ai aj funct c0 c1 1 22 2 0.1470 8.7100e+06 2 3 2 0.1090 1.2300e+07 2 4 2 0.1390 8.6600e+06 2 18 2 0.1435 6.1000e+06 4 5 2 0.1520 5.4300e+06 4 23 2 0.1435 6.1000e+06 5 6 2 0.1230 1.6600e+07 5 7 2 0.1380 1.1000e+07 7 8 2 0.1000 1.8700e+07 7 9 2 0.1400 8.5400e+06 9 10 2 0.1400 8.5400e+06 9 13 2 0.1320 1.2000e+07 10 11 2 0.1000 1.8700e+07 10 12 2 0.1000 1.8700e+07 13 14 2 0.1000 1.8700e+07 15 16 2 0.1435 6.1000e+06 15 17 2 0.1480 5.7300e+06 15 27 2 0.1390 8.6600e+06 16 18 2 0.1435 6.1000e+06 16 25 2 0.1435 6.1000e+06 17 19 2 0.1390 8.6600e+06 17 33 2 0.1390 8.6600e+06 18 31 2 0.1435 6.1000e+06 19 20 2 0.1090 1.2300e+07 19 21 2 0.1330 1.0600e+07 21 22 2 0.1360 4.7700e+06 22 33 2 0.1350 1.0300e+07 23 24 2 0.1090 1.2300e+07 23 25 2 0.1390 1.0800e+07 25 26 2 0.1090 1.2300e+07 27 28 2 0.1090 1.2300e+07 27 29 2 0.1435 6.1000e+06 29 30 2 0.1090 1.2300e+07 29 31 2 0.1390 1.0800e+07 31 32 2 0.1090 1.2300e+07 33 34 2 0.1090 1.2300e+07 [ pairs ] ; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp 2 6 1 2 7 1 4 8 1 4 9 1 5 10 1 5 13 1 6 8 1 6 9 1 6 23 1 7 11 1 7 12 1 7 14 1 7 23 1 8 10 1 8 13 1 10 14 1 11 13 1 12 13 1 16 19 1 16 33 1 19 27 1 27 33 1 [ angles ] ; ai aj ak funct angle fc 3 2 4 2 120.00 390.00 3 2 18 2 120.00 390.00 4 2 18 2 120.00 560.00 2 4 5 2 120.00 560.00 2 4 23 2 120.00 560.00 5 4 23 2 125.00 750.00 4 5 6 2 121.00 685.00 4 5 7 2 115.00 610.00 6 5 7 2 124.00 730.00 5 7 8 2 116.00 465.00 5 7 9 2 125.00 750.00 8 7 9 2 115.00 460.00 7 9 10 2 110.00 1280.00 7 9 13 2 120.00 560.00 10 9 13 2 125.00 750.00 9 10 11 2 116.00 465.00 9 10 12 2 115.00 460.00 11 10 12 2 109.50 285.00 9 13 14 2 109.50 285.00 16 15 17 2 120.00 560.00 16 15 27 2 120.00 560.00 17 15 27 2 120.00 560.00 15 16 18 2 120.00 560.00 15 16 25 2 125.00 750.00 18 16 25 2 120.00 560.00 15 17 19 2 132.00 760.00 15 17 33 2 126.00 640.00 19 17 33 2 105.00 1320.00 2 18 16 2 120.00 560.00 2 18 31 2 120.00 560.00 16 18 31 2 120.00 560.00 17 19 20 2 126.00 575.00 17 19 21 2 111.00 530.00 20 19 21 2 120.00 505.00 19 21 22 2 106.00 1690.00 1 22 21 2 119.00 1210.00 1 22 33 2 125.00 750.00 21 22 33 2 112.00 1400.00 4 23 24 2 120.00 390.00 4 23 25 2 120.00 560.00 24 23 25 2 120.00 390.00 16 25 23 2 120.00 560.00 16 25 26 2 120.00 390.00 23 25 26 2 120.00 390.00 15 27 28 2 120.00 390.00 15 27 29 2 120.00 560.00 28 27 29 2 120.00 390.00 27 29 30 2 120.00 390.00 27 29 31 2 120.00 560.00 30 29 31 2 120.00 390.00 18 31 29 2 120.00 560.00 18 31 32 2 120.00 390.00 29 31 32 2 120.00 390.00 17 33 22 2 108.00 465.00 17 33 34 2 131.00 927.00 22 33 34 2 121.40 690.00 [ dihedrals ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc 15 27 29 31 2 0.00 167.36 27 29 31 18 2 0.00 167.36 29 31 18 16 2 0.00 167.36 31 18 16 15 2 0.00 167.36 18 16 15 27 2 0.00 167.36 16 15 27 29 2 0.00 167.36 17 19 21 22 2 0.00 167.36 19 21 22 33 2 0.00 167.36 21 22 33 17 2 0.00 167.36 22 33 17 19 2 0.00 167.36 33 17 19 21 2 0.00 167.36 16 25 23 4 2 0.00 167.36 25 23 4 2 2 0.00 167.36 23 4 2 18 2 0.00 167.36 4 2 18 16 2 0.00 167.36 2 18 16 25 2 0.00 167.36 18 16 25 23 2 0.00 167.36 15 16 17 27 2 0.00 167.36 16 15 18 25 2 0.00 167.36 17 15 19 33 2 0.00 167.36 27 15 28 29 2 0.00 167.36 18 2 16 31 2 0.00 167.36 25 16 23 26 2 0.00 167.36 31 18 29 32 2 0.00 167.36 2 3 4 18 2 0.00 167.36 29 27 30 31 2 0.00 167.36 23 4 24 25 2 0.00 167.36 4 2 5 23 2 0.00 167.36 33 17 22 34 2 0.00 167.36 19 17 20 21 2 0.00 167.36 5 4 6 7 2 0.00 167.36 9 7 10 13 2 0.00 167.36 7 5 8 9 2 0.00 167.36 22 1 21 33 2 0.00 167.36 [ dihedrals ] ; ai aj ak al funct ph0 cp mult 2 4 5 7 1 180.00 33.50 2 4 5 7 9 1 180.00 33.50 2 5 7 9 13 1 180.00 33.50 2 13 9 10 11 1 180.00 33.50 2 7 9 13 14 1 180.00 33.50 2 16 15 17 33 1 180.00 1.53 2 [ exclusions ] ; ai aj funct ; GROMOS 1-4 exclusions 1 17 1 19 1 34 2 15 2 24 2 25 2 29 2 32 3 5 3 16 3 23 3 31 4 16 4 26 4 31 5 18 5 24 5 25 15 20 15 21 15 22 15 23 15 26 15 30 15 31 15 34 16 24 16 28 16 29 16 32 17 18 17 25 17 28 17 29 18 23 18 26 18 27 18 30 19 34 20 22 20 33 21 34 24 26 25 27 25 31 27 32 28 30 28 31 30 32 -- With Regards Monoj Mon Kalita Institute of Biophotonics<http://www.ym.edu.tw/biophotonics/eng_version/home.htm> Fischer's Lab <http://www.ym.edu.tw/%7Ewfischer/group_mon.htm> National Yang-Ming University<http://nymu-e.web.ym.edu.tw/front/bin/home.phtml> Taipei, Taiwan mon.123c...@gmail.com -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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