On Wed, Dec 11, 2013 at 1:11 AM, rajat desikan <rajatdesi...@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 <jalem...@vt.edu> wrote:
>
> > On Tue, Dec 10, 2013 at 8:55 AM, rajat desikan <rajatdesi...@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
> >
> > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> >
> >
> > ==========================================
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 

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

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441


==========================================
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Reply via email to