I had exactly this problem. The reason was I've edited mdp file at Windows. Sounds silly, I know, but just do your editing for mdp at Linux, it solved the problem for me.
Yulia Einav Ph.D. ________________________________ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Q733 Sent: Saturday, August 11, 2007 5:36 AM To: [email protected] Subject: [gmx-users] a basic question 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
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