[gmx-users] Strange trjconv error

[rajat desikan]

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'

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.

Thanks.

-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore