Alright sounds good to me. In order to make it sure once again....I have to do something like this... awk -f atom2cg.awk 1K4C.pdb > 1K4C_cg.pdb
and then....to get the .gro file.... genbox -cp 1K4C_cg.pdb -box 10 10 10 -o 1K4C_cg.gro and then...... grompp -f em.mdp -c 1K4C_cg.gro -p 1K4C.top -maxwarn 10 AM I CORRECT? Sunny On Tue, Aug 18, 2009 at 7:44 PM, Justin A. Lemkul <[email protected]> wrote: > > > sunny mishra wrote: > >> Hi Justin, >> >> I am using these commands... >> >> genbox -cp 1K4C.pdb -box 10 10 10 -o 1K4C.gro >> >> from here I can get my 1K4C.gro file. >> >> As far as CG structure of protein is concerned I can produce the CG >> structure using awk script like this.. >> >> awk -f atom2cg.awk 1K4C.pdb > 1K4C_CG.pdb >> >> But after getting the CG structure its difficult to get the .itp file for >> 1K4C_CG.pdb because dssp does not produce .ssd files for CG structure of >> proteins and if I am not having .ssd file then i cant get 1K4C_CG.itp file >> so thats why I did not use awk script and I was just doing for the normal >> protein to test first. >> >> > You need the awk script to generate the CG structure. You use the > atomistic structure to get the .ssd information - you've done this > correctly. > > Here is the error------------ >> >> grompp -f em.mdp -c 1K4C.gro -p 1K4C.top -maxwarn 10 >> > > <snip> > > >> NOTE 1 [file em.mdp, line unknown]: >> For energy conservation with switch/shift potentials, rlist should be 0.1 >> to 0.3 nm larger than rcoulomb. >> >> NOTE 2 [file em.mdp, line unknown]: >> For energy conservation with switch/shift potentials, rlist should be 0.1 >> to 0.3 nm larger than rvdw. >> > > Pay attention to these notes! > > processing topology... >> Generated 0 of the 465 non-bonded parameter combinations >> Excluding 1 bonded neighbours molecule type 'Protein' >> NOTE 3 [file 1K4C.top, line 15]: >> System has non-zero total charge: 4.000000e+00 >> >> >> processing coordinates... >> >> ------------------------------------------------------- >> Program grompp, VERSION 4.0.5 Source code file: >> grompp.c, line: 362 >> Fatal error: >> number of coordinates in coordinate file (1K4C.gro, 4534) >> does not match topology (1K4C.top, 1166) >> >> > Now this makes sense. You are using an atomistic structure (1K4C.gro) with > a CG topology. The structure input into grompp should be the CG structure > that comes from the awk script. > > -Justin > > >> >> >> On Tue, Aug 18, 2009 at 7:24 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> sunny mishra wrote: >> >> Ok. Thanks but I am doing a small test to make the .top file and >> .gro files of fresh 1K4C protein structure without removing >> anything but when I run my grommp command to minimize it as I >> asked earlier as well it says number of atoms in the .top are >> not equal to .top file and as you said that without adding any >> other molecule I just have to fix the [molecules] section, but >> it doesn't fix. >> >> here are some details of my .top file which I created on my own >> after getting the 1K4C.itp file. I got 1K4C.itp file something >> like this.. >> >> grep -A 1 1K4C 1K4C.txt > 1K4C.seq (This generates 1K4C.seq) >> dsspcmbi 1K4C.pdb 1K4C.dssp (gives 1K4c.dssp) >> dssp2ssd.py 1K4C.dssp -o 1K4C.ssd (this gives 1K4C.ssd) >> >> seq2itp.pl 1K4C.seq 1K4C.ssd > 1K4C.itp >> >> >> <snip> >> >> >> and after that I produce my 1K4C.gro file from genbox or >> editconf and then when i run the command grommp it says that >> number of atoms in .gro >> >> >> What commands are you giving genbox/editconf? You've never invoked >> the awk script that converts an atomistic protein structure to CG >> (provided by the MARTINI folks). Could that be the cause of the >> disconnect? Without seeing the actual error message, the best >> anyone can do is guess. >> >> -Justin >> >> file are unequal to .top file. Since I am doing the simulation >> in vacuum I cannot add anything else. Don't know how to proceed. >> >> Thanks, >> >> Sunny >> >> On Tue, Aug 18, 2009 at 7:00 PM, Justin A. Lemkul >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> wrote: >> >> >> >> sunny mishra wrote: >> >> Hi all, >> >> Is there anyway I can generate the .gro file from .top file >> without using the command pdb2gmx and editconf? >> >> >> A .top file is a topology - atomic descriptions; a .gro is a >> coordinate file. They are unrelated and therefore cannot be >> inter-converted. >> >> -Justin >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected] >> >> >> >> http://lists.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] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>. >> >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> 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://lists.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 >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> http://lists.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] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> 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 >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> http://lists.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] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.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 >> > > -- > ======================================== > > 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 > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.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 >
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