[gmx-users] plzz help
I am doing simulation of membrane protein in lipid bi layer for my college project!. can you please elaborate on the shrinking step that needs to be iterated to get the right protein per lipid area. thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
I am doing simulation of membrane protein in lipid bilayer for my college project!. After making the complex of protein and lipid bilayer, I was going to the step using genbox to solvate the system. The error that i am now getting is : Fatal error: Not enough memory. Failed to realloc 1008588696 bytes for nlist-jjnr, nlist-jjnr=0x20026008 (called from file ns.c, line 537) what should i do?? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
i am doing protein in bilipid membrane simulation. while packing the protein in the lipid membrane step, i am getting this error. command : perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Reading. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 300. please help!! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] help!!
i am using the tutorial KALP15 in DPPC for my protein in bilipid membrane SIMULATION. i have reached Step Three: Defining the Unit Cell Adding Solvent where i hav to pack the lipids around the protein using InflateGro. how do i start using inflategro? my last step was : to generate this new position restraint file using genrestr: genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 After which ,In the .mdp file used for the minimizations, i added a line define = -DSTRONG_POSRES to make use of these new position restraints. when i next gave the command :perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat ERROR Can't open perl script inflategro.pl: No such file or directory WHAT SHOULD I DO??? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fatal error: atom C not found in buiding block 19NH2 while combining tdb and rtp
i am stimulting an AMP protein in water. this is the error i get on my first step.. pdb2gmx -f 1PG1_1.pdb -o 1PG1_1_processed.gro -water spce error: Fatal error: atom C not found in buiding block 19NH2 while combining tdb and rtp please HELP!! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] em fatal error!
*We are trying to do simulation of lysozyme in water.* step with problem : energy minimization. command given: *[root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr* :-) G R O M A C S (-: Getting the Right Output Means no Artefacts in Calculating Stuff :-) 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 minim.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c 1AKI_solv_ions.gro InputStructure 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 topol.top InputTopology file -pp processed.top Output, Opt. Topology file -o em.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 -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool 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 Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 1641 *Fatal error: No such moleculetype NA* what should we do -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
