[gmx-users] non-standard residues in pdb2gmx

Hey everyone, I have a .pdb file that I need to convert to .gmx. The tricky thing is that the protein has a lipid bound to the N-terminus, which pdb2gmx doesn't recognize. The lipid is a myristic acid residue (14:0), and I haven't been able to find it in any database. What would be the most stra

[gmx-users] pdb2gmx bug?

nyone seen this before? Any ideas as to what could be causing this, or is it maybe a bug? Thanks for your help Gard Nelson ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] umbrella sampling in gromacs

Hi all, I'd like to calculate the PMF for a small molecule moving from a membrane-bound protein into the membrane itself. I tried using the "cylinder" option for pull_geometry, but when I tried to analyze the results with g_wham it said that "cylinder" isn't a supported option. Is this correct?

[gmx-users] segmentation fault with grompp

any ideas of what might be causing this? Thanks Gard Nelson -- gmx-users mailing listgmx-users@gromacs.org 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. U

[gmx-users] Re: segmentation fault with grompp

Ok, here's what i've got: Gromacs version 4.0.5. Both platforms are Linux, icc 10, fftw 3 compile option: ./configure --enable-mpi thanks for your help! Gard Gard Nelson wrote: > Hi all, > I'm trying to simulate a solvated membrane using Berger's lipids. When

[gmx-users] segmentation fault with grompp

lem, or is it just me? What can I do to find and fix the problem? Thanks Gard Nelson -- gmx-users mailing listgmx-users@gromacs.org 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)subscr

[gmx-users] segmentation fault with grompp

Ok, here's my topology file: ; Include forcefield parameters #include "ffgmx.itp" #include "lipid.itp" ; Include Lipid Topologies #include "popc.itp" ; Include water topology #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct

[gmx-users] g_wham error

Hi all, I'm trying to analyze a series of umbrella sampling windows, but I get the following error: Program g_wham, VERSION 4.0.7 Source code file: gmx_wham.c, line: 1397 Fatal error: Found 1 pull groups in onePREP0.tpr, but 1 data columns in onePREP0.xvg (expected 6) my .mdp file is: title

[gmx-users] g_wham error

Here's my .xvg: # This file was created Mon Mar 8 01:50:07 2010 # by the following command: # /opt/apps/intel10_1/mvapich1_1_0_1/gromacs/4.0.5/bin/mdrun_mpi -multi 31 -deffnm onePREP -px onePREP -np 2976 -maxh 3 # # /opt/apps/intel10_1/mvapich1_1_0_1/gromacs/4.0.5/bin/mdrun_mpi is part of G R O M