Re: [gmx-users] simulating hydrocarbons in water

2007-10-10 Thread Adam Fraser
Ah, okay thanks very much! I thought-sure I had the most recent version, but apparently not. Still there's one quirk... x2top -f HexA.gro -o HexA.top -r HexA.rtp -alldih ...This works to generate a topology file, but still, the program is seg-faulting before writing out the residue type file (*.

Re: [gmx-users] simulating hydrocarbons in water

2007-10-10 Thread Adam Fraser
Much appreciated, works beautifully! On 10/10/07, TJ Piggot <[EMAIL PROTECTED]> wrote: > > Just as a note editconf will covert a pdb to a gro file > > Tom > > --On Wednesday, October 10, 2007 09:47:03 -0400 Adam Fraser > <[EMAIL PROTECTED]> wrote: > > > Yes I tried this and it doesn't work for me.

Re: [gmx-users] simulating hydrocarbons in water

2007-10-10 Thread TJ Piggot
Just as a note editconf will covert a pdb to a gro file Tom --On Wednesday, October 10, 2007 09:47:03 -0400 Adam Fraser <[EMAIL PROTECTED]> wrote: Yes I tried this and it doesn't work for me. I get: Fatal error: Library file ffG53a6.n2t not found in current dir nor in default directories.

Re: [gmx-users] simulating hydrocarbons in water

2007-10-10 Thread David van der Spoel
Adam Fraser wrote: Yes I tried this and it doesn't work for me. I get: Fatal error: Library file ffG53a6.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) did you use 3.3.2 ? The default and only supported FF ther

Re: [gmx-users] simulating hydrocarbons in water

2007-10-10 Thread Adam Fraser
Yes I tried this and it doesn't work for me. I get: Fatal error: Library file ffG53a6.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) Also, doesn't x2top take in a gro file? (not a pdb) I wrote a script that convert

Re: [gmx-users] simulating hydrocarbons in water

2007-10-10 Thread David van der Spoel
Adam Fraser wrote: Hello, I'm very new to Gromacs, and I am interested in simulating the interactions of 2 hexadecane (C16H34) molecules in water (SPC/E specificall). I've spent some time experimenting with tutorials in Gromacs, but I've found little help in non-protein simulations like this

[gmx-users] simulating hydrocarbons in water

2007-10-10 Thread Adam Fraser
Hello, I'm very new to Gromacs, and I am interested in simulating the interactions of 2 hexadecane (C16H34) molecules in water (SPC/E specificall). I've spent some time experimenting with tutorials in Gromacs, but I've found little help in non-protein simulations like this one. I've built topolo