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 :)
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I can't seem to get this to work out so I think I'm giving up and asking for
some big help. I've been trying to generate a poly(gamma-benzyl-L-glutamate)
with 5 and 10 repeat units but nothing seems to work out. Is there anyone that
would be generate a pdb file that would actually work with p
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
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.
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 :)
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 :)
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 mol
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
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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 s
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