[gmx-users] Strange trjconv error

[Justin Lemkul]

On Wed, Dec 11, 2013 at 1:11 AM, rajat desikan <rajatdesikan at gmail.com>wrote:

> Dear Justin,
>
> Thanks for the suggestion.
>
> Producing a .trr in catdcd still failed because it apparently produces a
> trajectory without a timestamp. So, I loaded the .dcd into vmd and saved
> the coordinates in a .trr file. This worked like a charm :)
>
> Note to self: Install gromacs with the vmd plugin next time...
>
>
That's certainly useful, but note that trjconv can deal perfectly well with
catdcd-produced .trr files, because trjconv can add timestamps with the -t0
and -timestep options.

-Justin


>
> On Tue, Dec 10, 2013 at 8:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> > On Tue, Dec 10, 2013 at 8:55 AM, rajat desikan <rajatdesikan at gmail.com
> > >wrote:
> >
> > > Hi All,
> > > I have a NPT NAMD trajectory of a membrane-protein that I want to
> analyze
> > > in gromacs 4.6.3. (g_density). I used catdcd to convert the .dcd to
> .pdb
> > > and generated a .top from the .psf using topotools in vmd. I then
> > generated
> > > a .tpr using grompp
> > >
> > > When I do any simple gromacs command like:
> > >
> > > trjconv -f 130ns-141ns.pdb -s ref.tpr -o 130ns-141ns.xtc
> > >
> > > I get the following error:
> > >
> > > Fatal error:
> > > An input file contains a line longer than 4096 characters, while the
> > buffer
> > > passed to fgets2 has size 4096. The line starts with: '20s'
> > >
> > >
> > Unfortunately this is an output bug, so the '20s' is not actually useful
> to
> > you.  Looks like something needs to be fixed in fgets2().
> >
> >
> > > wc -L ref.tpr
> > > >20344 ref.tpr
> > >
> > > The gmxdump of the .tpr along with grep gave me the offending line. It
> is
> > > essentially the protein description:
> > >
> > > atom[     0]={type=  0, typeB=  0, ptype=    Atom, m= 1.40067e+01,
> > > q=-6.00000e-01, mB= 1.40067e+01, qB=-6.00000e-01, resind=    0,
> > atomnumber=
> > > -1}
> > >             atom[     1]={type=  0, typeB=  0, ptype=    Atom, m=
> > > 1.20107e+01, q=-1.00000e-01, mB= 1.20107e+01, qB=-1.00000e-01, resind=
> > > 0, atomnumber= -1}
> > >             atom[     2]={type=  0, typeB=  0, ptype=    Atom, m=
> > > 1.20107e+01, q=-3.50000e-01, mB= 1.20107e+01, qB=-3.50000e-01, resind=
> > > 0, atomnumber= -1}
> > >             atom[     3]={type=  0, typeB=  0, ptype=    Atom, m=
> > > 1.20107e+01, q=-3.50000e-01, mB= 1.20107e+01, qB=-3.50000e-01, resind=
> > > 0, atomnumber= -1}
> > >             atom[     4]={type=  0, typeB=  0, ptype=    Atom, m=
> > > 1.20107e+01, q=-3.50000e-01, mB= 1.20107e+01, qB=-3.50000e-01, resind=
> > > 0, atomnumber=
> > >
> > >
> >
> -1}...........................................................................
> > >
> > > Any idea about how to proceed. I am quite stumped.
> > >
> > >
> > The problem is not in the .tpr file, it is in the .pdb file.  Something
> > about its format is bad.  Why not use catdcd to produce a .trr file
> > instead?
> >
> > -Justin
> >
> > --
> >
> > ==========================================
> >
> > Justin A. Lemkul, Ph.D.
> > Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >
> >
> > ==========================================
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>
>
>
> --
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
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-- 

==========================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


==========================================