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 -- 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.