Dear Gromacs users, I am trying to transform my PDP file for AL2O3 surface to a top file using x2top. I have defined my forcefield.itp and .n2t file. However, I keep recieving an error telling me that "Could only find a forcefield type for 0 out of 66 atoms"
my PDB file looks like COMPND UNNAMED AUTHOR GENERATED BY OPEN BABEL 2.3.2 CRYST1 4.759 8.243 17.151 90.00 90.00 90.00 P1 1 HETATM 1 O LIG 1 3.201 0.667 3.490 1.00 0.00 O HETATM 2 O LIG 1 0.822 4.789 3.490 1.00 0.00 O HETATM 3 O LIG 1 0.822 2.041 7.821 1.00 0.00 O HETATM 4 O LIG 1 3.201 6.163 7.821 1.00 0.00 O HETATM 5 B LIG 1 3.201 3.415 12.151 1.00 0.00 B HETATM 6 B LIG 2 0.822 7.536 12.151 1.00 0.00 B HETATM 7 O LIG 1 1.017 1.928 3.490 1.00 0.00 O HETATM 8 O LIG 1 3.397 6.050 3.490 1.00 0.00 O HETATM 9 O LIG 1 3.397 3.302 7.821 1.00 0.00 O HETATM 10 O LIG 1 1.017 7.424 7.821 1.00 0.00 O my itp file looks like #define _ff_clayff [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.5 [ atomtypes ] ; name mass charge ptype sigma eps ho 1 1.00800 0.4250 A 0.00000e-01 0.00000e-01 ;clayFF_hydroxylhydrogen 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_bridgingoxyge ao 13 26.98200 1.5750 A 4.27128e-01 6.0e-06 ;ClayFF_octahedalaluminium [ bondtypes ] ; i j func b0 kb oh ho 1 0.1000 554134.9 [ angletypes ] ; i j k func th0 cth ao oh ho 1 109.47 125.52 my .n2t file looks like B oh -0.9500 15.998 1 H 0.100 ;hydroxyl oxygen O ob -1.2996 15.998 0 ;bridging oxygen with double substitution H ho -1.0808 15.998 1 B 0.100 ;hydroxyl hydrogen with substitution AL ao 1.5750 26.982 0 ;octahedral aluminium Your help is really appreciated Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.