Fwd: [gmx-users] Invalid atom number 6415 in indexfile
Liu Shiyong
liushiyong at gmail.com
Thu Jan 29 18:03:22 CET 2009
On Wed, Jan 28, 2009 at 6:32 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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.
*.gro has no chain id information.
I can not make energy group(based on chain id) from *.gro file generated by
pdb2gmx
>
> 3. Don't strip H, just to add them back again :)
I have the structure minimized.pdb after EM.
minimized.pdb is output from mdrun with -c option.
I tried to feed this structure into pdb2gmx.
I got an error.
Processing chain 1 'A' (5360 atoms, 535 residues)
There are 803 donors and 760 acceptors
There are 1025 hydrogen bonds
Will use HISB for residue 212
Will use HISB for residue 223
Will use HISB for residue 277
Will use HISB for residue 280
Will use HISB for residue 374
Will use HISB for residue 380
Will use HISB for residue 386
Will use HISB for residue 398
Will use HISB for residue 425
Will use HISB for residue 440
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../../src/kernel/pdb2gmx.c, line: 421
Fatal error:
Atom HD1 in residue HISB 212 not found in rtp entry with 14 atoms
while sorting atoms. Maybe different protonation state.
Remove this hydrogen or choose a different protonation state.
Option -ignh will ignore all hydrogens in the input.
-------------------------------------------------------
"You Could Be a Shadow" (The Breeders)
>
>
> Hopefully this makes sense.
>
> -Justin
>
> "God is a DJ" (Faithless)
>>
>>
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>>
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>>
>>
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>>
>>
>>
>>
>>
>> On Wed, Jan 28, 2009 at 12:28 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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>
>> <mailto: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> <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> <mailto:syliu at ku.edu
>> <mailto:syliu at ku.edu>> (shiyongliu at ku.edu
>> <mailto:shiyongliu at ku.edu> <mailto:shiyongliu at ku.edu
>> <mailto:shiyongliu at ku.edu>> or liushiyong at ku.edu
>> <mailto:liushiyong at ku.edu> <mailto:liushiyong at ku.edu
>> <mailto:liushiyong at ku.edu>>)
>>
>> Homepage: http://www.people.ku.edu/~syliu<http://www.people.ku.edu/%7Esyliu>
>> <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: 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><
>> 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 <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
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> --
> ========================================
>
> 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
>
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
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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