Fwd: [gmx-users] Invalid atom number 6415 in indexfile
Liu Shiyong
liushiyong at gmail.com
Thu Jan 29 01:15:03 CET 2009
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.
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
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
*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
make_ndx -f clean2.pdb -o clean2_0.6.ndx < ./make_ndx.input >
clean2_0.6.output.make_ndx 2>&1
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
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
-------------------------------------------------------
"God is a DJ" (Faithless)
On Wed, Jan 28, 2009 at 12:28 PM, Justin A. Lemkul <jalemkul at vt.edu> 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 <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> 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> | (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: syliu at ku.edu <mailto:syliu at ku.edu> (shiyongliu at ku.edu <mailto:
>> shiyongliu at ku.edu> or liushiyong at ku.edu <mailto:liushiyong at ku.edu>)
>> 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 | (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: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
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: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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