Yi Hou wrote:
Thank you very much, yes normally, the header of pdb file has remark 465 and
470. I just used the modeller loop to add the missing residues according to
remark 470, and did not add following remark 465, is it right? because
Normally one has to deal with *both* missing residues and missing atoms.
Ignoring parts of this section can generate frustrations in trying to set up the
system, or worse, incorrect answers, depending on the nature of what's missing.
there are only RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER,
it does not have atoms. By the way, there is a limit for modeller loop, if I
want to addd more resiudes, are there any others softwares which are
recommended.
I haven't used Modeller much, but there certainly are programs out there. Loopy
comes to mind, but I haven't done much loop building lately. Probably a simple
Google search and look through relevant homology modeling and other simulation
literature will turn up some useful programs.
-Justin
Thank you very much
Yi
On 03/08/2009 17:12, "Justin A. Lemkul" <jalem...@vt.edu> wrote:
Yi Hou wrote:
Dear Justin
Thank you very much
My commands are:
1. add hydrogens, get top and gro files
pdb2gmx -f 1z92.pdb -o 1z92.gro -p 1z92.top
If I'm not mistaken, 1z92 has substantial stretches of missing residues, and
you
probably had to model them in. I'd look at those regions as being potentially
problematic.
2. specify the box size, and add water to the system
editconf -f 1z92.gro -bt cubic -d 0.7 -o box.gro
genbox -cp box.gro -cs spc216.gro -p 1z92.top -o sol.gro
3. grommpp -f em.mdp -p 1z92.top -c sol.gro -o em.tpr then found the system
is charge -3
4. add 3NA+ ions in the SOL system
genion -s em.tpr -p 1z92.tpr -p 1z92.top -o sol_ion.gro -pname NA+ -np 3
-nname CL- -nn 0 -random
5. perform the energy minimization simulation
grompp -f em.mdp -p 1z92.top -o sol_ion.gro -o em.tpr
mdrun -deffnm em -v
Those commands until now then I should do position constraints and equil
simulations with my pr.mdp and md.mdp parameters.
I will check my .log file again to see if any errors occur
I'd stop and diagnose why the minimization failed. If you can't finish EM,
there is no point in running any sort of dynamics, equilibration or otherwise.
-Justin
Thank you very much
Yi
On 03/08/2009 15:56, "Justin A. Lemkul" <jalem...@vt.edu> wrote:
houyi wrote:
Dear all,
I guess others have the same problem for me as well, and it may repeat
to ask it again due to i am new for gromacs- 3.3.3. my protein is
1z92.pdb. when i perform the energy minimization , i got this error. but
when i used for another small protein, which is 1ycr.pdb, it worked well
for all. i choose the OPLS-AA/L all-atom force field
my em.mdp is
title = protein
cpp = /usr/bin/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 100
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01
i found the website and some one said change the table extension to 2 or
3 or maybe more, it works for this step, but after performing the
postion constrains, it got the wrong results. so i guess i will not
change the table extension, and i do not why it only work for small
protein not for larger one, and i repeated sevel times, such as changing
timesteps and rlist and rcoulomb and rvdw to 0.9. still not working.
could anyone help me to explain this.
Your system is blowing up due to some non-physical interaction. Tweaking
the
table-extension is probably not going to help. Some general references:
http://oldwiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-o
ff
http://oldwiki.gromacs.org/index.php/blowing_up
Without knowing more about how you prepared the system (exact commands),
then
you will not likely get much more useful advice. Take a look at where
things
are falling apart (atom numbers printed in the .log file) and see if you can
deduce the source of the problem.
-Justin
thank you very much
Reards,
Yi
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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