Hello,
I am posting this summary in case anyone else encounters the same
problem. Replies were received from David A. Case, Morpholino Peligro,
Arunabh Athreya, Tushar R. and Walker Olivier (through Adriana Miele).
The problem: how to get MD runs when you are not a specialist (first
time you have to "do it") and that it all must be free.
The version of Maestro linked to Desmond is licensed and therefore it
isn't possible to use it here;
Gromacs: im my hands, trying to compile from source (and therefore get a
parallelized version) failed, and the version distributed for my Linux
flavour failed to execute properly the examples given on the internet;
Suggestion to use VMD and NAMD: VMD doesn't install on my Linux box
somehow and the tutorials I found require both VMD and NAMD;
CHARMM: there was a suggestion to use the CHARMM forum, which may be
useful? Somehow my registration wasn't accepted by the system and the
reason isn't made available to the person who tries to register.
Then there was this final suggestion that was useful: CHARMM-GUI.
At first I was trying to use setup.inp and this failed repeatedly.
What worked was pdbreader on the CHARMM-GUI web site, the pdb passes
through all the stages of preparation and in the end produces two input
file, one for equilibration (step 4?) and the second one for a MD run
(step 5?).
Since the CHARMM-GUI web site is a CHARMM web site I chose to produce
input files for- and run- CHARMM (and not the other software for which
input files can also be produced): in case of failure(s) I wouldn't know
if these would be due to incorrect input files being produced or to
problems with the software on my box. Safest probably.
Thanks to those who replied.
Also note that vi cannot be used as an editor with CHARMM input files.
Nedit will do but not vi.
Fred.
Hi folks,
Sorry about the non-ccp4 question. I don't know where to ask.
I have to perform MD simulations but I am totally on my own here.
The
one program that appears to be free (in terms of license) seems to
be
CHARMM. GROMACS (testing with the examples found in the internet)
did
not work in my hands so I forget about that.
Charmm somehow looks similar to a program I used to work with,
X-PLOR.
However I haven't found a manual similar to the old XPLOR manual nor
a
web site that can generate the input files as was the case for
X-PLOR.
Neither did I find anywhere a flow chart allowing me to know which
steps
to be performed and in what order.
Hence: does anyone know of an X-PLOR to CHARMM dictionary ? Or a
CHARMM
bulletin board similar to CCP4BB ?
Just to give an example using the CHARMM setup.inp file for a
protein
that has an "ACE" cap at the N-terminus: fails. It complains about
the
ACE cap. Removing the cap solves that problem but then CHARMM fails
because of "HIS". If CHARMM fails because it doesn't like any
amino-acids then I don't know how I can use the program. But still
I'd
like to use it because I have to.
Thanks,
Fred.
--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic
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