[gmx-users] topology and residue database?

Is there still a topology and peptide residue on the Gromacs website? It's mentioned in the documentation but I can't seem to find it. Thanks :) _ Hotmail® has ever-growing storage! Don’t worry about storage limits.

[gmx-users] Making a .pdb file that actually works?

I've tried multiple times to make a pdb file that will work with pdb2gmx. I've even drawn the molecule into PRODRG but the structure will still not work. I simply want a poly(benzyl-L-glutamate) with 5 repeat units. How in the world can I get this to work? Thank you for your time.

[gmx-users] pdb does not work.

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

[gmx-users] best way to generate .pdb files?

I am currently using chembiodraw to draw my molecular structure but it does not generate an adequate pdb file. what is the best way to make them? i feel like my only hold back right now is the pdb file. thank you for your help :)

[gmx-users] how to run with mpi?

i have a small cluster of 3 computers, 1 master and 2 slaves, running Rocks 4.2.1 and Gromacs 3.3.1. Are there any good tutorials about how to use openmpi and Gromacs? I'm rather new to this so any help would be amazing. Thank you :)

[gmx-users] Where are the good tutorials?

Are there any good tutorials that start from the very beginning, like assuming you only have a .pdb file? It seems that most of the tutorials I've found have already generated the files you need and then all you have to do is punch in some commands. Where can I learn to actually write the

[gmx-users] How to create .pdb files?

I have tried to export .pdb files from ChemBio3D Ultra but it does not do a very good job. What is the best or simply a good, reliable method of generating a .pdb file? Thanks for your help :) Casey _ Insert movie times and more

[gmx-users] Pull Peptide Apart

Hello All, I'm fairly new to GROMACS so I apologize for if the question is simple. I have a small peptide that I would like to pull apart. What is the process for doing this? What type of things should I be reading into? Is there any tutorials or code already for such a process? I've