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 <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.