<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">What's the name for DNA under [ moleculetype ] in your top file?</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Another question is: have you included ffamber_tip3p.itp?</DIV>
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<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Probably you need to post excerpt of your topology here if you are not sure about your answers towards above two questions.</DIV>
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<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Regards,</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Yang Ye<BR><BR></DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">----- Original Message ----<BR>From: Anna Reymer <anna.reymer@gmail.com><BR>To: gmx-users@gromacs.org<BR>Sent: Wednesday, June 20, 2007 10:57:28 PM<BR>Subject: [gmx-users] grompp or parameter file problem?<BR><BR>
<DIV>Hello all!<BR><BR>I am trying to simulate DNA dodecamer in TIP3P water with Amber 99 port.<BR>I was ablle to produce dna+solvent.top (attached file) and dna+solvent.gro.<BR>When running grompp:<BR><BR>grompp -f em.mdp -c dna+solvent.gro -p dna+solvent.top -o out.tpr<BR><BR>with the following em.mdp:<BR>-------------------------------------<BR>; DNA energy minimization in water<BR>;<BR>cpp = /lib/cpp -traditional<BR>define =<BR>include = -I/***/share/gromacs/top/ffamber99.itp<BR>constraints = none<BR>integrator = cg<BR>nsteps = 1000<BR>;<BR>; ENERGY MINIZATION
STUFF<BR>;<BR>emtol = 2000<BR>emstep = 0.01<BR>nstcgsteep = 100<BR>nstcomm = 1<BR>ns_type = grid<BR>rlist = 1<BR>rcoulomb = 1.0<BR>rvdw = 1.0<BR>Tcoupl = no<BR>Pcoupl = no<BR>gen_vel = no<BR><BR>I get the fatal error message:<BR>Program grompp, VERSION 3.3.1<BR>Source code file: grompp.c, line: 448<BR><BR>Fatal error:<BR>number of coordinates in coordinate file (genbox.gro,
32804)<BR> does not match topology (dick.top, 0)<BR>-------------------------------------------------------<BR>Top file has all includes and its tail looks:<BR><BR><BR>[ molecules ]<BR>; Compound #mols<BR>Protein 1<BR>SOL 10682<BR>---------------------------------------------------------<BR>Does somebody have similar problems? Has somebody solved them?<BR><BR>I will appreciate any help!<BR><BR>regards<BR>/anna<BR>_______________________________________________<BR>gmx-users mailing list gmx-users@gromacs.org<BR><A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A
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