You probably need to define [atomtypes] before you can define [bondtypes] that use them. So swap the order of your #include statements.
Mark On Mon, Oct 6, 2014 at 6:18 AM, Atila Petrosian <atila.petros...@gmail.com> wrote: > Dear gromacs users > > I want to do MD simulation of a CNT. > > I used aromatic carbon from charmm.ff > > I created a cnt.ff folder containing following files: > > ffcnt.atp: > ----------- > CA 12.01100 ; aromatic C > ------------------------------------------------------------------------- > ffcnt.n2t: > ----------- > C CA 0.00 12.011 3 C 0.141 C 0.141 C 0.141 > C CA 0.00 12.011 2 C 0.141 C 0.141 > ------------------------------------------------------------------------- > ffcntbonded.itp: > -------------------- > [ bondtypes ] > ; i j func b0 kb > CA CA 1 0.1375 0.0 > > [ angletypes ] > ; i j k func th0 cth ub0 cub > CA CA CA 5 120.00 0.0 0.24162 29288.0 > > [ dihedraltypes ] > ; i j k l func phi0 cp mult > CA CA CA CA 9 180.00 0.0 2 > ------------------------------------------------------------------------- > ffcntnonbonded.itp: > ------------------------- > [ atomtypes > ] > ;name at.num mass charge ptype sigma > epsi > CA 6 12.01100 0.00 A 0.335 > 0.234463 > ------------------------------------------------------------------------- > ffcnt.rtp: > ---------- > [ bondedtypes > ] > ; Col 1: Type of > bond > ; Col 2: Type of > angles > ; Col 3: Type of proper > dihedrals > ; Col 4: Type of improper > dihedrals > ; Col 5: Generate all dihedrals if 1, only heavy atoms of > 0. > ; Col 6: Number of excluded neighbors for nonbonded > interactions > ; Col 7: Generate 1,4 interactions between pairs of hydrogens if > 1 > ; Col 8: Remove propers over the same bond as an improper if it is > 1 > ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 > RemoveDih > 1 5 9 2 1 3 1 > 0 > > > [ ALA > ] > [ atoms > ] > N NH1 -0.47 > 0 > HN H 0.31 > 1 > CA CT1 0.07 > 2 > HA HB 0.09 > 3 > CB CT3 -0.27 > 4 > HB1 HA 0.09 > 5 > HB2 HA 0.09 > 6 > HB3 HA 0.09 > 7 > C C 0.51 > 8 > O O -0.51 > 9 > . > . > . > ------------------------------------------------------------------------- > forcefield.itp: > ---------------- > #define _FF_CNT > > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 2 yes 1.0 1.0 > > #include "ffcntbonded.itp" > #include "ffcntnonbonded.itp" > ------------------------------------------------------------------------- > > After creating cnt.top file using g_x2top, I used grompp for energy > minimization, but I encountered with Fatal Error: > > Syntax error - File ffcntbonded.itp, line 1 > Last line read: > '[ bondtypes ]' > Invalid order for directive bondtypes > > Before doing MD simulation, I checked carbon nanotube in the GROMACS > website: > > > http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube?highlight=nanotube > > In my opinion, my manner is true. > > How to solve this problem? > > Any help will highly appreciated. > -- > 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. > -- 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.