Hi Justin and Mark, I just realized that I have some missing atoms in my .gro file when I compared with .itp file and may be this is causing the problem. The atoms which are missing what should I do with them. Should I delete both from .itp and .gro file OR do i have to add in my .gro file and if I have to add them then how?
for example in my .itp file there are 2 ILE but in my .gro file there is only 1 ILE. So should i add another ILE in my .gro file or delete 2 ILE from .itp and 1ILE from .gro. Thanks in advance. Sunny On Wed, Aug 19, 2009 at 7:23 PM, sunny mishra <[email protected]>wrote: > > 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 >> > >
_______________________________________________ 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
