Hi, Thank you for your advise. I am aware of the IED webpage and that's what drew my attention to the Angstrom, nm issue!
However I had run pca without any conversion and my structure didn't get distorted, all analysis returns structures in Angstrom that don't appear out of place but what I am concerned with is whether the movements are masked because gromacs thinks that atoms are 10 times further away?! I tried that patch but couldn't see any difference! (having said that I couldn't directly apply the patch, so I just went into trxio.c and edited the lines by hand and then recompiled) Thank you, Nadia Vahdati J.W.Essex University of Southampton UK. Quoting Florian Haberl <[EMAIL PROTECTED]>: > On Thursday 05 October 2006 16:56, [EMAIL PROTECTED] wrote: > > Hi gromacs users, > > > > I am a new user to gromacs and realise that there are lots of comments > on > > the archive already about using gromacs with amber outputs but I am > getting > > rather mixed messages. > > > > I would like to clarify a few things. I have an Amber trjectory file > saved > > through VMD in a .pdb format and a pdb file for the topology. > > > > I see that some say that one should convert the trajectory file, some > say > > that gromacs reads .pdb and others mention changing the extension to > .g87 > > and so on. My main question is about the fact that amber works in > > Angstroms and gromacs in nm. Should I convert my trajectory.pdb and > > topology.pdb to nm before carrying out principal component analysis? > > > > I would be grateful for any comments. > > take a look at > > http://mccammon.ucsd.edu/ied/ > > Notes for using GROMACS to analyze AMBER trajectories > > These notes are of mostly historical interest, now that IED is able to > read > output from Ptraj. In general it will be easier to analyze AMBER > trajectories > with Ptraj than with GROMACS. > > GROMACS can be used to analyze trajectories produced by the SANDER module > of > AMBER. GROMACS will read the AMBER trajectory if it is renamed to have an > extension of .g87 . GROMACS will not read the AMBER prmtop topology file, > but > you can produce a pdb file to use as the topology file like this > > ambpdb -p prmtop <prmcrd >topol.pdb > > There is one problem with using GROMACS to analyze AMBER data: GROMACS > assumes > coordinates are in nanometers, while AMBER writes them in Angstroms.You > can > ignore this problem, in which case all your atoms will be ten times > further > apart than they should be in IED. Since VMD uses distances to determine > bonding for PDB files, this means that if you use a PDB topology file, > you > won't see any bonds. If you use the van der Waals representation (with an > increased radius) and remember to divide any distances you measure by 10, > this may be acceptable. > > If you are comfortable with recompiling GROMACS, you can use the > following > patch so that your distances will be correct and bonds will appear. Note > that > with this patch, all .g87 files are assumed to be in units of Angstroms, > so > if you think you may actually need to read a .g87 file in units of > nanometers, this may not be a good idea. > > The following patch should be applied to src/gmxlib/trxio.c > > --- trxio.c 2002-02-28 02:49:31.000000000 -0800 > +++ trxio.c 2003-12-12 17:11:34.000000000 -0800 > @@ -453,14 +453,14 @@ > /* else eof! */ > return FALSE; > } > - x[i][m]=x0; > + x[i][m]=x0 * 0.1; > } > } > if (bReadBox) { > for(m=0; (m<DIM); m++) { > if (fscanf(status,"%lf",&x0) != 1) > return FALSE; > - box[m][m]=x0; > + box[m][m]=x0 * 0.1; > } > } > return TRUE; > > > > It should be also possible to save a multiple pdb file and than read it > with > gromacs and convert it to gromacs style trajectory. > > > > > > Thank you in advance, > > > > Nadia Vahdati > > > > J.W.Essex group > > University of Southampton > > UK. > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > Greetings, > > Florian > > -- > ------------------------------------------------------------------------------- > Florian Haberl > Computer-Chemie-Centrum > Universitaet Erlangen/ Nuernberg > Naegelsbachstr 25 > D-91052 Erlangen > Telephone: +49(0) â 9131 â 85 26581 > Mailto: florian.haberl AT chemie.uni-erlangen.de > ------------------------------------------------------------------------------- > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
