Hi Mark, I am sorry that I was not accurate in my scripts and I will not repeat this mistake again. Justin advised me that if the atoms are missing in .itp file and .gro file (Some of them are actually missing) then I have to model the atoms back in the ORIGINAL PDB file but I din't quite get him. Can you help me out with this that how to model the original PDB file (1K4C) before I proceed.
Thanks, Sunny On Wed, Aug 19, 2009 at 8:25 PM, Mark Abraham <[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. >> > > Justin's advice was also very sound. If your model lacks relevant atoms, > you have more work to do. Surely the MARTINI scripts should be providing > some warnings here? > > I got the 1K4C_cleanCG.seq file using grep command like this >> >> grep -A 1 1K4c_clean CG 1K4C_cleanCG.txt > 1K4C_cleanCG.seq >> > > Nobody's interested in what your command was "like". This also was not your > command, since you've added a space to make "1K4c_clean CG" and still not > given it a filename suffix. Write a script so you've got a reliable record, > or copy and paste from your terminal. Accuracy and reproducibility are > critically important. > > Mark > > 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. >> >> Thanks, >> >> Sunny >> >> On Wed, Aug 19, 2009 at 6:54 PM, Justin A. Lemkul <[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.organd >>>>> 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] >>>> 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 >>> >>> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 >
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