Hi Gromacs users
I have a problem Im trying to form a .top file using a g_x2top -f -o -ff command. I have defined .n2t .rtp .itp files. and wanted to construct a topology file. but the script does not identify any of the atoms from .gro file. my .n2t file ; clayff ; n2t H h* 0.4100 1.008 1 O 0.100 ;water hydrogen H ho 0.4250 1.008 1 O 0.100 ;hydrxyl hydrogen O o* -0.8200 15.998 2 H 0.100 H 0.100 ;water oxygen O oh -0.9500 15.998 1 H 0.100 ;hydroxyl oxygen O ob -1.0500 15.998 0 ;bridging oxygen O obos -1.1808 15.998 0 ;bridging oxygen with octahedral substitution O obts -1.1688 15.998 0 ;bridging oxygen with tetrahedral substitution O obss -1.2996 15.998 0 ;bridging oxygen with double substitution O ohs -1.0808 15.998 1 H 0.100 ;hydroxyl hydrogen with substitution Si st 2.1000 28.086 0 ;tetrahedral silicon Al ao 1.5750 26.982 0 ;octahedral aluminium Al at 1.5750 26.982 0 ;tetrahedral aluminium Mg mgo 1.3600 24.305 0 ; octahedral magnisium Na Na 1.0000 22.999 0 ;sodium ion my.itp file ; ; [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 ; parameters are taken from the clay force field [ atomtypes ] ; The charges here will be overwritten by those in the rtp file ; name mass charge ptype sigma eps h* 1 1.00800 0.4100 A 0.00000e-01 0.00000e-01 ;clayFF_waterhydrogen ho 1 1.00800 0.4250 A 0.00000e-01 0.00000e-01 ;clayFF_hydroxylhydrogen o* 8 15.99800 -0.8200 A 3.16557e-01 6.50209e-01 ;ClayFF_wateroxygen oh 8 15.99800 -0.9500 A 3.16557e-01 6.50209e-01 ;ClayFF_hydroxyloxygen ob 8 15.99800 -1.0500 A 3.16557e-01 6.50209e-01 ;ClayFF_bridgingoxygen obos 8 15.99800 -1.1808 A 3.16557e-01 6.50209e-01 ;ClayFF_bridgingoxygenoctasub obts 8 15.99800 -1.1688 A 3.16557e-01 6.50209e-01 ;ClayFF_bridgingoxygentetrsub ohs 8 15.99800 -1.0808 A 3.16557e-01 6.50209e-01 ;ClayFF_hydroxyloxygensub st 14 28.08600 2.1000 A 3.30208e-01 8.0e-06 ;ClayFF_tetrahedralsilicon ao 13 26.98200 1.5750 A 4.27128e-01 6.0e-06 ;ClayFF_octahedalaluminium at 13 26.98200 1.5750 A 3.30206e-01 8.0e-06 ;ClayFF_tetrasubaluminium mgo 12 24.30500 1.3600 A 5.26437e-01 4.0e-06 ;ClayFF_octasubmagnisium Na 11 22.999 1.0000 A 1.89744e-01 6.72427e-01 ;ClayFF_Na [ bondtypes ] ; i j func b0 kb oh ho 1 0.10000 463711.2 ; O-H ohs ho 1 0.10000 463711.2 ; O-H o* h* 1 0.10000 463711.2 ; O-H [ angletypes ] ao oh ho 1 109.470 251.046 ; angle Al-O-H mgo ohs ho 1 109.470 251.046 ; angle Mg-O-H h* o* h* 1 109.470 383.009 ; angle H-O-H [ dihedraltypes ] my .gro file 1Created by VESTA 2808 Clay ao 1 0.005 0.564 -0.021 Clay ao 2 -0.602 0.564 3.099 Clay ao 3 4.226 0.564 -0.021 Clay ao 4 3.620 0.564 3.099 Clay st 5 0.178 0.254 0.256 Clay ob 6 0.175 0.240 0.090 Clay ob 7 0.201 0.411 0.296 Clay ob 8 0.037 0.622 0.318 Clay oh 9 0.192 -0.046 0.090 Clay oh 10 0.192 3.610 0.090 Clay ho 11 0.099 -0.046 0.151 Clay ho 12 0.099 3.610 0.151 Clay st 13 0.058 0.254 1.263 Clay ob 14 0.061 0.240 1.429 Clay ob 15 0.035 0.411 1.222 Clay ob 16 0.199 0.622 1.200 Clay oh 17 0.044 -0.046 1.429 Clay oh 18 0.044 3.610 1.429 Clay ho 19 0.136 -0.046 1.368 Clay ho 20 0.136 3.610 1.368 Clay ao 21 0.005 0.259 -0.021 Clay ao 22 -0.602 0.259 3.099 Clay ao 23 4.226 0.259 -0.021 Clay ao 24 3.620 0.259 3.099 Clay st 25 0.058 0.568 1.263 Clay ob 26 0.061 0.582 1.429 Clay ob 27 0.199 0.200 1.200 Clay st 28 0.178 0.568 0.256 Clay ob 29 0.175 0.582 0.090 Clay ob 30 0.037 0.200 0.318 Clay ao 31 0.268 0.107 -0.021 Clay ao 32 -0.338 0.107 3.099 could any one please let me know what might be the problem best Milinda Samaraweera University of Connecticut Department of Chemistry 55 N Eagleville road unit 3060 Storrs CT USA -- 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. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
