<P>
<BR>
Hello Mark,<BR>
<BR>
I have again started working on CORE_MTB.pdb<BR>
<BR>
The first step that I took was <BR>
<BR>
1. pdb2gmx -f CORE_MTB.pdb -o CORE_MTB.gro -p CORE_MTB.top<BR>
<BR>
<BR>
It has generated fatal error as follows<BR>
<BR>
Fatal error:<BR>
Atom HD1 in residue HISB 61 not found in rtp entry with 12 atoms<BR>
while sorting atoms. Maybe different protonation state.<BR>
Remove this hydrogen or choose a different protonation state.<BR>
Option -ignh will ignore all hydrogens in the input.<BR>
<BR>
Then I used -ignh option and the steps are as follows..<BR>
<BR>
<BR>
2. editconf -f CORE_MTB.gro -o CORE_MTB.gro -d 0.8<BR>
<BR>
WARNING: No boxtype specified - distance condition applied in each dimension.<BR>
If the molecule rotates the actual distance will be smaller. You might want<BR>
to use a cubic box instead, or why not try a dodecahedron today?<BR>
<BR>
3. genbox -cp CORE_MTB.gro -cs -o CORE_MTB_b4em.gro -p CORE_MTB.top<BR>
<BR>
4.grompp -f em.mdp -po em_out.mdp -c CORE_MTB_b4em.gro -p CORE_MTB.top -o CORE_MTB_em.tpr<BR>
<BR>
<BR>
5.mdrun -s CORE_MTB_em.tpr -o CORE_MTB_em.trr -c CORE_MTB_b4pr.gro -e em.edr -g em.log<BR>
<BR>
After this I got some message with output as follows<BR>
<BR>
Steepest Descents converged to machine precision in 15 steps,<BR>
but did not reach the requested Fmax < 2000.<BR>
Potential Energy = 2.1868101e+17<BR>
Maximum force = inf on atom 28916<BR>
Norm of force = nan<BR>
<BR>
Could you please tell me what is wrong ?<BR>
<BR>
The mdp file used for grompp amd mdrun is as follows..<BR>
<BR>
<BR>
<BR>
; User spoel (236)<BR>
; Wed Nov 3 17:12:44 1993<BR>
; Input file<BR>
;<BR>
cpp = /usr/bin/cpp<BR>
define = -DFLEX_SPC<BR>
constraints = none<BR>
integrator = steep<BR>
nsteps = 100<BR>
;<BR>
; Energy minimizing stuff<BR>
;<BR>
emtol = 2000<BR>
emstep = 0.01<BR>
<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>
<BR>
<BR>
On Tue, 13 Dec 2005 Mark Abraham wrote :<BR>
>Dhananjay joshi wrote:<BR>
>> Yes Mark,<BR>
>><BR>
>>You are right.<BR>
>><BR>
>>using "gmx_dump -s CORE_MTB_em.tpr | less" i found large vector of velocities (v) after the large vector of positions (x) and that they are all non-zero.<BR>
>><BR>
>>what should I do now ?<BR>
><BR>
>>>see if there is a large vector of velocities (v) after the large vector of positions (x) and that they are all zero. If they aren't, I suspect you haven't actually done as you describe above.<BR>
><BR>
>grompp is the only thing that can be generating velocities. Check you've done what you think you've done.<BR>
><BR>
>Mark<BR>
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