Re: [gmx-users] pdb does not work.

2009-06-15 Thread Mark Abraham
Joseph Johnson wrote: Just as a test run I wanted to see if I could simulate 5 repeats of glycine. I give the command: pdb2gmx -f PGly.pdb -p PGly.top -o PGly.gro and I tell it to do: 0: GROMOS96 43a1 force field The output I get is: Program pdb2gmx, VERSION 3.3.1 Source code file: resall.

RE: [gmx-users] pdb does not work.

2009-06-15 Thread Dallas B. Warren
Because pdb2gmx has to know what residue(s) are contained in the .pdb file, and the third column identifies the residue and as the program has told you, it is called "1". And it does not have a "1" residue on the .rtp file associated with that forcefield. Catch ya, Dr. Dallas Warren Department o

[gmx-users] pdb does not work.

2009-06-15 Thread Joseph Johnson
Just as a test run I wanted to see if I could simulate 5 repeats of glycine. I give the command: pdb2gmx -f PGly.pdb -p PGly.top -o PGly.gro and I tell it to do: 0: GROMOS96 43a1 force field The output I get is: Program pdb2gmx, VERSION 3.3.1 Source code file: resall.c, line: 438 Fatal err