Alright. Sounds good to me. let me check that out and i will let you know the progress. Thanks,
Sunny On Wed, Aug 19, 2009 at 7:19 PM, Justin A. Lemkul <[email protected]> wrote: > > > sunny mishra wrote: > >> Hi Mark and Justin, >> >> Thanks for the valuable advise and I want to do the last test but before I >> proceed I just want to make sure If I am doing everything correct. >> >> I got the 1K4C_cleanCG.seq file using grep command like this >> >> grep -A 1 1K4c_clean CG 1K4C_cleanCG.txt > 1K4C_cleanCG.seq >> >> Now my next step is to get the .ssd file for 1K4C_cleanCG.pdb which I >> cannot get and in that case I have to use 1K4C_clean.pdb in order to get >> .ssd file. >> >> And If i am correct here then my next step would be to get the .itp file >> for 1K4C_cleanCG. So my last question is that when I will use seq2itp.pl >> script which .seq file should I use and which .ssd file should I use to get >> the output .itp file. I mean this.... >> >> seq2itp.pl 1K4C_cleanCG.seq 1K4C_clean.ssd > 1K4C_cleanCG.itp >> >> OR >> seq2itp.pl 1K4C_clean.seq 1K4C_clean.ssd > 1K4C_clean.itp >> >> In the first command I don't think I can get the .ssd file( >> 1K4C_cleanG.ssd ) so thats why I am using 1K4C_clean.ssd. Now I dnt know if >> I am doing this wrong or correct but before proceeding i want to ask you >> guys to correct me at this point. >> >> > The .seq file should not depend at all on anything to do with the > structure; the amino acid sequence is invariant. You can download the FASTA > sequence from the PDB and use that (accounting for any missing terminal > residues); it shouldn't make a difference. > > -Justin > > Thanks, >> >> Sunny >> >> On Wed, Aug 19, 2009 at 6:54 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> In addition to everything Mark said, also realize that there may be >> a fundamental problem in everything you are doing: there are missing >> atoms in the original 1K4C structure. If you have not modeled them >> back in, the appropriate CG particles will not necessarily all be >> placed in your CG structure, but the topology will be written such >> that it expects all the correct atoms to be there. >> >> At first glance, Arg117 is going to cause headaches - it is missing >> all atoms beyond CB, and since CG and NE are necessary for MARTINI's >> definition of an ARG residue, you can bet this will be a problem. >> >> -Justin >> >> >> Mark Abraham wrote: >> >> sunny mishra wrote: >> >> Hi Justin, >> >> Thanks for the reply and here is the following which I am >> doing. I would >> appreciate if you can point out my errors. >> >> >> 1) I am working on 1K4C (KcSA) and i downloaded that from >> www.pdb.org <http://www.pdb.org> and >> >> after that I cleaned the PBD file, removed all the HETATOMS >> and ATOMS with >> ligand A & B and also removed the TER atoms. So my cleaned >> PDB file i.e. >> (1K4C_clean.pdb) consists of atoms with ligands C and #of >> atoms are 765. >> >> 2) After getting the 1K4C_clean.pdb I converted the atomic >> structure to CG >> structure using awk script...something like this >> >> awk -f atom2cg.awk 1K4C_clean.pdb > 1K4C_cleanCG.pdb >> >> >> Here you create 1K4C_cleanCG.pdb >> >> 3) Then I got the sequence of 1K4C_clean.pdb using vmd and >> saved that as >> 1K4C_clean.txt and with the help of the following command I >> got the .seq >> file... >> >> >> But below you create your .itp starting from "1K4C_clean", which >> at least means you haven't copied your correct grep line, and >> might indicate the mismatch between your structure and topology. >> >> grep -A 1 1K4C_clean 1K4C_clean.txt > 1K4C_clean.seq >> >> 4) Then using dssp I got the .ssd file for 1K4C_clean.pdb.... >> >> dsspcmbi 1K4C_clean.pdb 1K4C_clean.dssp >> dssp2ssd.py 1K4C_clean.dssp -o 1K4C_clean.ssd >> >> 5) After preparing the secondary structure files I generated >> the MARTINI >> topology files like this : >> >> seq2itp.pl 1K4C_clean.seq 1K4C_clean.ssd > 1K4C_clean.itp >> >> 6) The next step is to make the topology file and I made >> like this..... >> >> ; Include Martini Topology >> #include "martini_v2.1.itp" >> >> ; Include protein topology >> #include "1K4C_clean.itp" >> >> >> [ system ] >> ; Name >> Membrane Protein >> >> [ molecules ] >> ; compound #mols >> Protein 1 >> >> 7) Then I made the .gro file using genbox..... >> >> genbox -cp 1K4C_cleanCG.pdb -box 10 10 10 -o 1K4C_cleanCG.gro >> >> (In the previous email as you said that I need to make the >> .gro file of CG >> structure of protein so I used 1K4C_cleanCG.pdb) >> >> >> A .gro file is almost never essential. A structure file with a >> suitable periodic box can be. >> >> 8) Now I want to minimize the system..... >> >> grompp -f em.mdp -c 1K4C_cleanCG.gro -p 1K4C_clean.top >> -maxwarn 10 >> >> and then error comes........... >> >> :-) G R O M A C S >> (-: >> >> GROningen MAchine for Chemical Simulation >> >> :-) VERSION 4.0.5 (-: >> >> >> Written by David van der Spoel, Erik Lindahl, Berk >> Hess, and others. >> Copyright (c) 1991-2000, University of Groningen, The >> Netherlands. >> Copyright (c) 2001-2008, The GROMACS development >> team, >> check out http://www.gromacs.org for more >> information. >> >> This program is free software; you can redistribute >> it and/or >> modify it under the terms of the GNU General Public >> License >> as published by the Free Software Foundation; either >> version 2 >> of the License, or (at your option) any later >> version. >> >> :-) grompp (-: >> >> Option Filename Type Description >> ------------------------------------------------------------ >> -f em.mdp Input, Opt! grompp input file with MD >> parameters >> -po mdout.mdp Output grompp input file with MD >> parameters >> -c 1K4C_cleanCG.pdb Input Structure file: gro g96 >> pdb tpr tpb tpa >> -r conf.gro Input, Opt. Structure file: gro g96 pdb >> tpr tpb tpa >> -rb conf.gro Input, Opt. Structure file: gro g96 >> pdb tpr tpb tpa >> -n index.ndx Input, Opt. Index file >> -p 1K4C_clean.top Input Topology file >> -pp processed.top Output, Opt. Topology file >> -o topol.tpr Output Run input file: tpr tpb tpa >> -t traj.trr Input, Opt. Full precision trajectory: >> trr trj cpt >> -e ener.edr Input, Opt. Energy file: edr ene >> >> Option Type Value Description >> ------------------------------------------------------ >> -[no]h bool no Print help info and quit >> -nice int 0 Set the nicelevel >> -[no]v bool yes Be loud and noisy >> -time real -1 Take frame at or first after >> this time. >> -[no]rmvsbds bool yes Remove constant bonded >> interactions with virtual >> sites >> -maxwarn int 10 Number of allowed warnings >> during input >> processing >> -[no]zero bool no Set parameters for bonded >> interactions >> without >> defaults to zero instead of >> generating an >> error >> -[no]renum bool yes Renumber atomtypes and minimize >> number >> of >> >> atomtypes >> >> Ignoring obsolete mdp entry 'title' >> Ignoring obsolete mdp entry 'cpp' >> Replacing old mdp entry 'unconstrained_start' by 'continuation' >> >> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8# >> checking input for internal consistency... >> >> 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. >> >> processing topology... >> Generated 0 of the 465 non-bonded parameter combinations >> Excluding 1 bonded neighbours molecule type 'Protein' >> >> NOTE 3 [file 1K4C_clean.top, line 15]: >> System has non-zero total charge: 2.000000e+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_cleanCG.pdb, >> 209) >> does not match topology (1K4C_clean.top, 216) >> ------------------------------------------------------- >> >> I don't know where I have done the mistake...your help will >> be highly >> appreciable in this case. >> >> >> Here you've got a 7-atom difference, and... >> >> >> ------------------------------------------------------- >> Program grompp, VERSION 4.0.5 >> Source code file: grompp.c, line: 362 >> >> Fatal error: >> number of coordinates in coordinate file >> (1K4C_cg.gro, 1127) >> does not match topology >> (1K4C.top, 1166) >> >> ------------------------------------------------------- >> >> >> ...here you're different by 39 atoms. That indicates a procedure >> that differed by more than just not adding solvent. >> >> With a complex multi-step system preparation, you are much >> better served by writing the steps down in a shell script so >> that you really do things the same way every time. Science is >> still science, even on a computer, and your work must be >> reproducible. Moreover, then when you ask for help, you're not >> presenting contradictions and non sequiturs that frustrate >> attempts to help you :-) >> >> In any case, my earlier advice still applies - it should be a >> matter of 10 minutes work to compare your clean .itp and .gro to >> see what atoms are causing the problem. Then, work backwards. >> >> Mark >> _______________________________________________ >> 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 >> >> >> > -- > ======================================== > > 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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