Liu Shiyong wrote:
Hi,
Thank for your helpful reply.
I understand your feeling. If you have time, please see the following.
mdrun has an option to output the final structure(-c). I just knew it
after reading your post and checked again :<
Thanks .
Firstly, I run a minimized command to get the minimized structure.
Secondly, based on the minimized structure, I want to do energy
calculation with some user-defined energy groups. I guest I need to run
second pdb2gmx.
I don't think you do. See comments below.
The command in the Step 1:
pdb2gmx -ff G53a6 -f r-l_207655_G53a6.pdb -p r-l_207655_G53a6.top
-i r-l_207655_G53a6.posre.itp -o r-l_207655_G53a6.gro >
r-l_207655_G53a6.output.pdb2gmx 2>&1
em.mdp
title =
r-l_207655_G53a6
cpp =
/usr/bin/cpp
define =
-DFLEX_SPC
constraints =
none
integrator =
l-bfgs
dt = 0.002 ; ps
!
nsteps =
10000
nstlist =
20
ns_type =
simple
rlist =
1.8
coulombtype =
shift
epsilon_r =
2.0
rcoulomb =
1.8
rcoulomb-switch =
1.7
vdwtype =
shift
rvdw =
1.5
rvdw_switch =
1.4
These are some bizarre cutoffs for use with 53a6, but perhaps you have your
reasons...
pbc =
no
;
; Energy minimizing
stuff
;
emtol =
100.0
emstep = 0.01
grompp -f em.mdp -c r-l_207655_G53a6.gro -p r-l_207655_G53a6.top -po
r-l_207655_G53a6.mdout.mdp -o r-l_207655_G53a6.input.tpr >
r-l_207655_G53a6.output.grompp
2>&1
mdrun -nice 0 -v -s r-l_207655_G53a6.input.tpr -o
r-l_207655_G53a6.minim_traj.trr -c r-l_207655_G53a6.minimized.pdb -e
r-l_207655_G53a6.minim_ener.edr -g r-l_207655_G53a6.emlog.log >
r-l_207655_G53a6.output.mdrun 2>&1
Now, I get an minimized structure: r-l_207655_G53a6.minimized.pdb
Then , I remove the Hydrogen atom in r-l_207655_G53a6.minimized.pdb,
rename as clean2.pdb
Why are you removing hydrogens?
*Step 2:*
Starting structure: clean2.pdb
I am trying to calculate the energy according to energy groups
pdb2gmx -ff G53a6 -f clean2.pdb -p clean2_0.6.top -i
clean2_0.6.posre.itp -o clean2_0.6.gro > clean2_0.6.output.pdb2gmx 2>&1
This is redundant. In the first pdb2gmx, you processed your structure with the
53a6 parameter set, adding some polar hydrogens and building a topology. Then,
you stripped the hydrogens. Now you are adding them back. I see no point in
all of these iterations.
make_ndx -f clean2.pdb -o clean2_0.6.ndx < ./make_ndx.input >
clean2_0.6.output.make_ndx 2>&1
Now you're using the original .pdb file (with no hydrogens) to make an index
group. *This is where you are probably going wrong* - you are carrying out EM
steps using a topology that includes H atoms on polar groups, but you are
constructing index groups that correspond to a structure without H. Therefore,
none of the atom numbers will correspond to what you think they are (or want
them to be).
em.mdp
title = clean2_0.6
cpp = /usr/bin/cpp
integrator = cg
dt = 0.002 ; ps !
nsteps = 1
rlist = 0.55
nstlist = 0
vdwtype = Cut-off
rvdw = 0.6
coulombtype = shift
epsilon_r = 20000
rcoulomb = 0.6
Again, really bizarre parameters for use with Gromos96.
rcoulomb-switch = 0.55
energy_grps = chB chA
;
; Energy minimizing stuff
;
emtol = 100.0
emstep = 0.01
grompp -maxwarn 10 -f em.mdp -c clean2_0.6.gro -n clean2_0.6.ndx -p
clean2_0.6.top -o clean2_0.6.input.tpr > clean2_0.6.output.grompp 2>&1
Then, I got an error msg:
clean2_0.6.output.grompp
-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: ../../../../src/kernel/grompp.c, line: 307
Fatal error:
atoms 4175 and 4183 in charge group 1767 are in different energy groups
-------------------------------------------------------
Right, because these two atoms were generated from a non-H structure, but you
are using the .gro and .top files (with H!) as input into grompp.
Here's what I'd recommend:
1. Run pdb2gmx and generate your 53a6 topology.
2. Make index groups from the .gro file generated by pdb2gmx.
3. Don't strip H, just to add them back again :)
Hopefully this makes sense.
-Justin
"God is a DJ" (Faithless)
On Wed, Jan 28, 2009 at 12:28 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Liu Shiyong wrote:
Hi,
Did you get my script ?
As I said just a few days ago, I don't run jobs for people. I only
have allocated time on our University's cluster, which I need for
myself.
That said, it is also very difficult to go through someone's
scripting, laden with variables that mean nothing to anyone else but
you, and come up with something meaningful, especially when everyone
on this list has their own work to be doing. As I've said several
times, simply posting your command lines with the relevant error
message(s) is sufficient.
That said, I really have no clue what you're doing with those
scripts. It appears that you are running pdb2gmx, grompp, and
mdrun, then using trjconv to dump out the last frame from your
energy minimization. The last step is certainly not necessary;
mdrun outputs the lowest-energy coordinates.
Then you are running pdb2gmx again, and creating index groups. I
don't understand the purpose of the second pdb2gmx call.
The problem you are facing is easily answered with the fact that you
simply are again using a structure file that does not have the same
number of atoms as the structure you used to create the index file.
It appears that your index files simply have two chains of a
protein, with the highest atom number being 5966. So of course atom
6415 is missing. The simple fix is to perhaps simplify your naming
strategy so you can keep it straight, or instead of scripting
everything and potentially making mistakes, to just run the commands
interactively until you have everything flowing.
-Justin
I dump a frame from .trr file.
I did not define xtc-grps
On Wed, Jan 21, 2009 at 2:00 PM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
Liu Shiyong wrote:
Hi,
I got an error when do grompp: The input PDB file
comes from
the output of GROMACS by trajconv command.
<snip>
-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: ../../../../src/kernel/readir.c, line: 838
*Fatal error:
Invalid atom number 6415 in indexfile*
-------------------------------------------------------
Instead of screen dumps, it would be a lot more useful to see
your
.mdp file, as well as the command line (not output from) both
grompp
and trjconv. Did you dump the frame from an .xtc file? What did
you specify in xtc-grps?
-Justin
-- ========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [email protected] <mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>> ([email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>> or [email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>)
Homepage: http://www.people.ku.edu/~syliu
<http://www.people.ku.edu/%7Esyliu>
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [email protected] <mailto:[email protected]> ([email protected]
<mailto:[email protected]> or [email protected] <mailto:[email protected]>)
Homepage: http://www.people.ku.edu/~syliu
<http://www.people.ku.edu/%7Esyliu>
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
--
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [email protected] <mailto:[email protected]> ([email protected]
<mailto:[email protected]> or [email protected] <mailto:[email protected]>)
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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