Re: [gmx-users] pdbgmx warning long bond

Hi Stéphane Can you give me a better explanation and provide files on your website ? Cheers Maite ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the lis

Re: [gmx-users] pdbgmx warning long bond

maite lopez a écrit : Dear Gromacs Users, I am trying to simulate a peptide in explicit lipid bilayer membrane environment (say, DPCC). I took well equilibrated dppc.pdb file from Dr. Peter tieleman site and i modified it put in the names of the atoms of the ffG53a5.rtp file . I changed DPPC x

Re: [gmx-users] pdbgmx warning long bond

Hi Maite, The thing is, if pdb2gmx does not encounter a TER statement or chain identifier, it usually tries to bind everything it finds together consecutively. So, you could try to add a number of TER statements, but still, it is better to generate the topology for your protein separately by runn

Re: [gmx-users] pdbgmx warning long bond

Hi Tsjerk: But, i think the problems is that pdb2gmx program see the membrane how a protein and it tries to tie the peptide with the membrane. The topology of dppc membrane appear in the ffG53a5.rtp file of gromacs. What can i do? Should i create a peptide.top file and include it a lipid.itp an

Re: [gmx-users] pdbgmx warning long bond

Greg, This likely does not reflect Maites problem. There was no mention of editing a pdb file to get the names right. Maite is dealing with lipids/protein, whereas you're dealing with DNA. That's a completely different topic, with particular problems, like the one you mention. Tsjerk On 1/25/07

Re: [gmx-users] pdbgmx warning long bond

I had the same problem few days ago (this was my first simulation too ;) when running a simulation on a standard B-DNA. I modified the names of atoms and residus in the pdb file of my dna to match G43a1.rtp names. Then when I run pdb2gmx I had the same warning. I tried to open the modified pdb

Re: [gmx-users] pdbgmx warning long bond

Hi Maite, pdb2gmx tries to tie your lipids together. Don't run the membrane through pdb2gmx. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___

[gmx-users] pdbgmx warning long bond

Dear Gromacs Users, I am trying to simulate a peptide in explicit lipid bilayer membrane environment (say, DPCC). I took well equilibrated dppc.pdb file from Dr. Peter tieleman site and i modified it put in the names of the atoms of the ffG53a5.rtp file . I changed DPPC x DPP in ffG53a5.rtp file