[gmx-users] pca on amber MD output

[nadiav at soton.ac.uk]

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 <Florian.Haberl at chemie.uni-erlangen.de>:

> On Thursday 05 October 2006 16:56, nadiav at soton.ac.uk 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.
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
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>
> Greetings,
>
> Florian
>
> --
>
-------------------------------------------------------------------------------
>  Florian Haberl
>  Computer-Chemie-Centrum
>  Universitaet Erlangen/ Nuernberg
>  Naegelsbachstr 25
>  D-91052 Erlangen
>  Telephone:  	+49(0) − 9131 − 85 26581
>  Mailto: florian.haberl AT chemie.uni-erlangen.de
>
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