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
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