Why you put a none in the include? It doesn't mean none when there is an "none".
Regards, Yang Ye On 8/11/2007 11:36 AM, Q733 wrote: > Hello everyone, I met with a problem today. I tried to simulate dppc > lipid in water.However, when I want to minimize energy ,the grompp > showed the error message like this: "number of coordinates in > coordinate file (box.gro 8253 ) doesn't match topology ( topol.top , 0 ). > I have used gromacs for sometime and checked the topology and itp file > carefully , but can't find out the problem.can anyone help me ? > here is the mdp file > title = > cpp = /lib/cpp -traditional-cpp > include = none > define = > constraints = none ;h-bonds > lincs_iter = 4 > ; RUN CONTROL PARAMETERS = > integrator = steep > tinit = 0 > dt = 0.001 ; ps > nsteps = 6000 > nstxtcout = 100 ; pos to xtc file > nstlist = 5 > ns_type = grid > rlist = 1.0 > coulombtype = PME > rcoulomb = 1.0 > vdw-type = Cut-off > rvdw = 1.0 > fourierspacing = 0.095 ; default to 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > ; ENERGY MINIMIZATION OPTIONS = > emtol = 100.0 ; default to 100 > emstep = 0.02 ; default to 0.01 > here is the topology file,and I have added the ffgmx forcefield into > "lipid1.itp" > #include "lipid1.itp" > #include "dppc.itp" > [ moleculetype ] > ; molname nrexcl > SOL 2 > [ atoms ] > ; nr type resnr residue atom cgnr charge mass > 1 OW 1 SOL OW 1 -0.82 15.99940 > 2 HW 1 SOL HW1 1 0.41 1.00800 > 3 HW 1 SOL HW2 1 0.41 1.00800 > > [ settles ] > ; OW funct doh dhh > 1 1 0.1 0.16330 > [ exclusions ] > 1 2 3 > 2 1 3 > 3 1 2 > [ system ] > ; name > DSPC in water > [ molecules ] > ; name number > DSP 64 > SOL 1599 > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > 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 _______________________________________________ gmx-users mailing list [email protected] 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
