[gmx-users] Strange trjconv error

[rajat desikan]

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...


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