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<DIV><FONT color=#000000 size=2 face=Arial>Dear all,</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>This must be a pretty simple problem but I am stuck nonetheless. I have been using the lipids from Prof Tieleman's website without any problem on gromacs 4.0.7. </FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=2 face=Arial>Now that I've got 4.5.3 installed, I want to try the g_membed tool but have encountered these problems.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=2 face=Arial>Following Justin's tutorial which gives a good tip on how to deal with the changes introduced in 4.5.3, these are the things I have done + the output</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>1) gave new names to the modified itp files from 4.0.7</FONT></DIV>
<DIV><FONT size=2 face=Arial>ffG53a6_lipid.itp to forcefield.itp</FONT></DIV>
<DIV><FONT size=2 face=Arial>ffG53a6nb_lipid.itp to ffnonbonded.itp</FONT></DIV>
<DIV><FONT size=2 face=Arial>ffG53a6bon_lipid.itp to ffbonded.itp</FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=2 face=Arial>2) created a folder gromos53a6_lipid.ff in the working directory to contain the files in (1)</FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=2 face=Arial>3) copied aminoacids.c.tdb, aminoacids.n.tdb, aminoacids.hdb, aminoacids.r2b, aminoacids.rtp, aminoacids.vsd, ff_dumitp, spc.itp, ions.itp, watermodels.dat from $GMXLIB into the gromos53a6_lipid.ff folder created in step (2). The created a forcefield.doc as instructed.</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>4) created .itp for my protein with pdb2gmx </FONT></DIV>
<DIV><FONT size=2 face=Arial><A href="mailto:huiwen3@magnum">huiwen3@magnum</A> 182% pdb2gmx -f protein_moved.pdb -o protein_pdb2gmx.pdb -p protein.top -ignh<BR> :-) G R O M A C S (-:</FONT></DIV>
<DIV><FONT size=2 face=Arial> Giant Rising Ordinary Mutants for A Clerical Setup</FONT></DIV>
<DIV><FONT size=2 face=Arial> :-) VERSION 4.5.3 (-:</FONT></DIV>
<DIV><FONT size=2 face=Arial> Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,<BR> Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,<BR> Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,<BR> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,<BR> Michael Shirts, Alfons Sijbers, Peter Tieleman,</FONT></DIV>
<DIV><FONT size=2 face=Arial> Berk Hess, David van der Spoel, and Erik Lindahl.</FONT></DIV>
<DIV><FONT size=2 face=Arial> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<BR> Copyright (c) 2001-2010, The GROMACS development team at<BR> Uppsala University & The Royal Institute of Technology, Sweden.<BR> check out <A href="http://www.gromacs.org">http://www.gromacs.org</A> for more information.</FONT></DIV>
<DIV><FONT size=2 face=Arial> This program is free software; you can redistribute it and/or<BR> modify it under the terms of the GNU General Public License<BR> as published by the Free Software Foundation; either version 2<BR> of the License, or (at your option) any later version.</FONT></DIV>
<DIV><FONT size=2 face=Arial> :-) pdb2gmx (-:</FONT></DIV>
<DIV><FONT size=2 face=Arial>Option Filename Type Description<BR>------------------------------------------------------------<BR> -f protein_moved.pdb Input Structure file: gro g96 pdb tpr etc.<BR> -o protein_pdb2gmx.pdb Output Structure file: gro g96 pdb etc.<BR> -p protein.top Output Topology file<BR> -i posre.itp Output Include file for topology<BR> -n clean.ndx Output, Opt. Index file<BR> -q clean.pdb Output, Opt. Structure file: gro g96 pdb etc.</FONT></DIV>
<DIV><FONT size=2 face=Arial>Option Type Value Description<BR>------------------------------------------------------<BR>-[no]h bool no Print help info and quit<BR>-[no]version bool no Print version info and quit<BR>-nice int 0 Set the nicelevel<BR>-chainsep enum id_or_ter Condition in PDB files when a new chain and<BR> molecule_type should be started: id_or_ter,<BR> id_and_ter, ter, id or interactive<BR>-ff string select Force field, interactive by default. Use -h for<BR> information.<BR>-water enum select Water model to use: select, none, spc, spce,<BR> tip3p, tip4p or tip5p<BR>-[no]inter bool no Set the next 8 options to interactive<BR>-[no]ss bool no Interactive SS bridge selection<BR>-[no]ter bool no Interactive termini selection, iso charged<BR>-[no]lys bool no Interactive Lysine selection, iso charged<BR>-[no]arg bool no Interactive Arganine selection, iso charged<BR>-[no]asp bool no Interactive Aspartic Acid selection, iso charged<BR>-[no]glu bool no Interactive Glutamic Acid selection, iso charged<BR>-[no]gln bool no Interactive Glutamine selection, iso neutral<BR>-[no]his bool no Interactive Histidine selection, iso checking<BR> H-bonds<BR>-angle real 135 Minimum hydrogen-donor-acceptor angle for a<BR> H-bond (degrees)<BR>-dist real 0.3 Maximum donor-acceptor distance for a H-bond (nm)<BR>-[no]una bool no Select aromatic rings with united CH atoms on<BR> Phenylalanine, Tryptophane and Tyrosine<BR>-[no]ignh bool yes Ignore hydrogen atoms that are in the pdb file<BR>-[no]missing bool no Continue when atoms are missing, dangerous<BR>-[no]v bool no Be slightly more verbose in messages<BR>-posrefc real 1000 Force constant for position restraints<BR>-vsite enum none Convert atoms to virtual sites: none, hydrogens<BR> or aromatics<BR>-[no]heavyh bool no Make hydrogen atoms heavy<BR>-[no]deuterate bool no Change the mass of hydrogens to 2 amu<BR>-[no]chargegrp bool yes Use charge groups in the rtp file<BR>-[no]cmap bool yes Use cmap torsions (if enabled in the rtp file)<BR>-[no]renum bool no Renumber the residues consecutively in the output<BR>-[no]rtpres bool no Use rtp entry names as residue names</FONT></DIV><FONT size=2 face=Arial>
<DIV><BR>Select the Force Field:<BR>From current directory:<BR> 1: GROMOS96 53A6 force field, extended to include Berger lipid parameters<BR>From '/usr/remote/gromacs/4.5.3/share/gromacs/top':<BR> 2: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)<BR> 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)<BR> 4: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)<BR> 5: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)<BR> 6: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)<BR> 7: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)<BR> 8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)<BR> 9: CHARMM27 all-atom force field (with CMAP) - version 2.0<BR>10: GROMOS96 43a1 force field<BR>11: GROMOS96 43a2 force field (improved alkane dihedrals)<BR>12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)<BR>13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)<BR>14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)<BR>15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<BR>16: [DEPRECATED] Encad all-atom force field, using full solvent charges<BR>17: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges<BR>18: [DEPRECATED] Gromacs force field (see manual)<BR>19: [DEPRECATED] Gromacs force field with hydrogens for NMR<BR></DIV>
<DIV>I selected 14 .... </DIV>
<DIV>Q: should I pick 1 instead?<BR></DIV></FONT>
<DIV><FONT size=2 face=Arial>5) combined protein and lipid structure files with cat protein_moved.pdb popc_solvated.pdb > merged.pdb, deleted some uneccessary lines and changed CRYST1 to that of the lipid </FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>6) Obtained a sample.mdp file from <A href="http://wwwuser.gwdg.de/~ggroenh/membed.html">http://wwwuser.gwdg.de/~ggroenh/membed.html</A></FONT><FONT size=2 face=Arial> called it g_membed_sample.mdp</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>7) did grompp -f sample.mdp -c merged.pdb -p merged.top -o input.tpr and got this error</FONT></DIV>
<DIV><FONT size=2 face=Arial> :-) G R O M A C S (-:</FONT></DIV>
<DIV><FONT size=2 face=Arial> Giant Rising Ordinary Mutants for A Clerical Setup</FONT></DIV>
<DIV><FONT size=2 face=Arial> :-) VERSION 4.5.3 (-:</FONT></DIV>
<DIV><FONT size=2 face=Arial> Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,<BR> Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,<BR> Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,<BR> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,<BR> Michael Shirts, Alfons Sijbers, Peter Tieleman,</FONT></DIV>
<DIV><FONT size=2 face=Arial> Berk Hess, David van der Spoel, and Erik Lindahl.</FONT></DIV>
<DIV><FONT size=2 face=Arial> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<BR> Copyright (c) 2001-2010, The GROMACS development team at<BR> Uppsala University & The Royal Institute of Technology, Sweden.<BR> check out <A href="http://www.gromacs.org">http://www.gromacs.org</A> for more information.</FONT></DIV>
<DIV><FONT size=2 face=Arial> This program is free software; you can redistribute it and/or<BR> modify it under the terms of the GNU General Public License<BR> as published by the Free Software Foundation; either version 2<BR> of the License, or (at your option) any later version.</FONT></DIV>
<DIV><FONT size=2 face=Arial> :-) grompp (-:</FONT></DIV>
<DIV><FONT size=2 face=Arial>Option Filename Type Description<BR>------------------------------------------------------------<BR> -f g_membed_sample.mdp Input grompp input file with MD parameters<BR> -po mdout.mdp Output grompp input file with MD parameters<BR> -c merged.pdb Input Structure file: gro g96 pdb tpr etc.<BR> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.<BR> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.<BR> -n index.ndx Input, Opt. Index file<BR> -p merged.top Input Topology file<BR> -pp processed.top Output, Opt. Topology file<BR> -o input.tpr Output Run input file: tpr tpb tpa<BR> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt<BR> -e ener.edr Input, Opt. Energy file</FONT></DIV>
<DIV><FONT size=2 face=Arial>Option Type Value Description<BR>------------------------------------------------------<BR>-[no]h bool no Print help info and quit<BR>-[no]version bool no Print version info and quit<BR>-nice int 0 Set the nicelevel<BR>-[no]v bool no Be loud and noisy<BR>-time real -1 Take frame at or first after this time.<BR>-[no]rmvsbds bool yes Remove constant bonded interactions with virtual<BR> sites<BR>-maxwarn int 0 Number of allowed warnings during input processing<BR>-[no]zero bool no Set parameters for bonded interactions without<BR> defaults to zero instead of generating an error<BR>-[no]renum bool yes Renumber atomtypes and minimize number of<BR> atomtypes</FONT></DIV><FONT size=2 face=Arial>
<DIV><BR>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#</DIV>
<DIV>NOTE 1 [file g_membed_sample.mdp]:<BR> nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting<BR> nstcomm to nstcalcenergy</DIV>
<DIV>Generated 165 of the 1596 non-bonded parameter combinations</DIV>
<DIV>-------------------------------------------------------<BR>Program grompp, VERSION 4.5.3<BR>Source code file: toppush.c, line: 1166</DIV>
<DIV>Fatal error:<BR>Atomtype LC3 not found<BR>For more information and tips for troubleshooting, please check the GROMACS<BR>website at <A href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</A><BR>-------------------------------------------------------</DIV>
<DIV>"Your Country Needs YOU" (U.S. Army)</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>8) My merged.top looks like this</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>; Include forcefield parameters<BR>#include "gromos53a6.ff/forcefield.itp"</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>;Include Protein Topology<BR>#include "protein.itp"</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>; Include Position restraint file<BR>#ifdef POSRES<BR>#include "posre.itp"<BR>#endif<BR>;<BR>;</FONT></DIV>
<DIV><FONT size=2 face=Arial>;Include POPC topology<BR>#include "popc.itp"<BR>;</FONT></DIV>
<DIV><FONT size=2 face=Arial>;Include water topology<BR>#include "gromos53a6.ff/spc.itp"</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>#ifdef POSRES_WATER<BR>; Position restraint for each water oxygen<BR>[ position_restraints ]<BR>; i funct fcx fcy fcz<BR> 1 1 1000 1000 1000<BR>#endif</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>; Include topology for ions<BR>#include "gromos53a6.ff/ions.itp"</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>[ system ]<BR>; Name<BR>POPC in water + Protein</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>[ molecules ]<BR>; Compound #mols<BR>Protein_X 1<BR>POPC 339<BR>SOL 16865<BR></FONT></DIV>
<DIV><FONT size=2 face=Arial>I am certain I have LC3 in the ffnonbonded.itp file I created in step (1)... </DIV></FONT>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>Many thanks for your help in advance.</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>Huiwen</FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV> <<
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