<DIV> Hi all:</DIV>
<P> I want to start simulation of protein that has heme group(FE).After learning the force field paremeter ,i add heme parameters to the force field's .rtp and .hdb file,and define a new bond </P>
<P>. i operated the gromacs command as followed.</P>
<P>1 pdb2gmx -ignh -ff G43a1 -f ffg43a1.pdb -o ffg43a1.pdb -p ffg43a1.top -water spce</P>
<P>2 editconf -bt cubic -f ffg43a1.pdb -o ffg43a1_cub.pdb -d 0.9</P>
<P>3 genbox -cp ffg43a1.pdb -cs spc216.gro -o ffg43a1_box.gro -p ffg43a1.top</P>
<P>and then i edit a em.mdp file:</P>
<P>title = ga431<BR>cpp = /lib/cpp</P>
<P>define = -DFLEXIBLE</P>
<P>constraints = none</P>
<P>integrator = steep</P>
<P>dt = 0.002 ; ps !</P>
<P>nsteps = 10</P>
<P>nstlist = 5</P>
<P>ns_type = grid</P>
<P>rlist = 0.9</P>
<P>coulombtype = PME</P>
<P>rcoulomb = 0.9</P>
<P>vdwtype = cut-off</P>
<P>rvdw = 1.4</P>
<P>fourierspacing = 0.12</P>
<P>fourier_nx = 0</P>
<P>fourier_ny = 0</P>
<P>fourier_nz = 0</P>
<P>pme_order = 4</P>
<P>ewald_rtol = 1e-5<BR>optimize_fft = yes<BR>;<BR>; Energy minimizing stuff<BR>;<BR>emtol = 1000.0<BR>emstep = 0.01</P>
<P>the nsteps =10 because i just want to go through it </P>
<P>and then i run command grompp</P>
<P>4 grompp -f em.mdp -c ffg43a1_box.gro -p ffg43a1.top -o ffg43a1.tpr</P>
<P>but a Fatal error emerged : There were 1 error(s) processing your input, <BR>i thought i made a wrong define of the heme residue,so i repeat the gromacs command using the protein without heme group.<BR>Unfortunately,the error comes again,with a difference of total charge (7.0 without heme,2.95 with heme)<BR>the error shows as followed:</P>
<P><BR>creating statusfile for 1 node...<BR>' for variable optimize_fft, using 'no'<BR>Next time use one of: 'no' 'yes'</P>
<P>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#<BR>checking input for internal consistency...<BR>calling /lib/cpp...<BR>processing topology...<BR>Generated 279 of the 1225 non-bonded parameter combinations<BR>Excluding 3 bonded neighbours for Protein 1<BR>Excluding 2 bonded neighbours for SOL 27299<BR>NOTE:<BR> System has non-zero total charge: 7.000003e+00</P>
<P>processing coordinates...<BR>double-checking input for internal consistency...</P>
<P>-------------------------------------------------------<BR>Program grompp, VERSION 3.3.3<BR>Source code file: grompp.c, line: 1132</P>
<P>Fatal error:<BR>There were 1 error(s) processing your input<BR>-------------------------------------------------------<BR> Does anyone help me amd tell me how to hand this problem??? i will go crazy!</P>
<P>thanks very very very much!!! </P>
<P> yours: jianli guo</P><BR><BR><SPAN title="neteasefooter">
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