[gmx-users] compatibility of MOPAC charges with GROMACS ?

Dear all I'm trying to assemble a topology entry for S-nitrosocysteine. Searching through the examples in the PDB revealed quite a spread of bond lengths and angles - the N=O bond ranges from 1.2 to 1.47A, for example. To get more rigorously derived figures, and to calculate charges, I thought of

[gmx-users] topology for nitrosylated cysteine?

Dear all Does anybody, by any chance, have a Gromacs topology file for a nitrosylated cysteine residue? If not, is anybody aware of information for this residue in other program packages, or will PRODRG be my best bet? Thanks in advance Daniel -- Dr Daniel John Rigden Tel

[gmx-users] gromacs -> amber trajectory conversion - resolution

Dear all Previously I (and others) have posted with issues regarding the conversion of gromacs trajectories (nm) to amber format (Angstrom). You can get g87 files form trjconv which are the same format as amber but in the wrong units. It turns out there is a simple way to do these conversions

[gmx-users] more on converting xtc to g87

Dear all I'm trying to convert an xtc to an Amber (g87) trajectory. I don't have the Amber package. trjconv makes a file which is read by the next package but I strongly suspect the bounding box information is wrong which in turn is likely to be to do with Gromacs working in nm, Amber in A. Fol

Re: [gmx-users] GROMACS compilation problem

> Erik > > On Apr 23, 2007, at 5:21 PM, Daniel Rigden wrote: > > > Dear all > > > > I'm trying to compile the latest GROMACS 3.3.1 on the latest Ubuntu > > Linux. Due to some fftw installation issue I used > > > > ./configure --with-fft=fftpa

[gmx-users] conversion of xtc to g87 (amber) format trajectory files/bounding box problem?

Hi everyone I'd like to convert my Gromacs trajectory to an Amber format for use with the CAVER program. Reading round, it seems that Amber is equivalent to the g87 format so I can use trjconv to produce the file. This all seems to work well (the file gets read in and processed) except for a prob

[gmx-users] GROMACS compilation problem

Dear all I'm trying to compile the latest GROMACS 3.3.1 on the latest Ubuntu Linux. Due to some fftw installation issue I used ./configure --with-fft=fftpack make make install All seemed to work fine, but any program I try to run now gives me a crash of this kind [EMAIL PROTECTED]: g_clustsiz

[gmx-users] published work on MD timescales/biological motions

Dear all This is a general MD question I'm afraid but I think this the quickest way to access an informed community. I remember seeing a while back an article that said that although MD simulations only extend to a timescale shorter than some biological motions, that these motions are typically qu