Hi,
On Wed, Jan 28, 2009 at 6:31 PM, Mark Abraham <[email protected]>wrote: > Liu Shiyong wrote: > >> Hi, >> > > >> *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>& >> > I tried to make energy groups from the "output" (*.gro) from pdb2gmx. > Found 0 atoms with chain identifier B Group is empty > Found 0 atoms with chain identifier A Group is empty That means no chain id information in *.gro, but I have to define the energy groups according to chain id . > >> So here you made some energy groups from the *input* to pdb2gmx. Make it > from the *output* from pdb2gmx and you will be sure things correspond to the > topology *output* from pdb2gmx. It seems rather obvious to me that your > input to make_ndx has all the hydrogens still in it. > > 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 <[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 >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>. >> >> 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: [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> >> <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>< >> 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<http://www.people.ku.edu/%7Esyliu> >> Lab: http://vakser.bioinformatics.ku.edu/people >> Phone: (785) 864-1962 >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > > 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: [email protected] ([email protected] or [email protected]) Homepage: http://www.people.ku.edu/~syliu Lab: http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962
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