[gmx-users] Flavone molecule
David van der Spoel
spoel at xray.bmc.uu.se
Fri Dec 26 10:16:01 CET 2003
On Fri, 26 Dec 2003, Semen Esilevsky wrote:
>Dear gmx users!
>Happy holidays to all!
>My question was probably discussed many times, but
>I have a custom molecule (flavone derivative) which
>has to be simulated in the lipid membrane. I have pdb
>coordinates for flavone, but there are no force field
>parameters for it. Is it enough to simulate it, or I
>have to construct forcefield? If yes how?
try the prodrg website to make a topology. link on www.gromacs.org
>--- Lieven Buts <lieven at ultr.vub.ac.be> wrote:
>> On Wednesday 24 December 2003 19:00, Claudio J.
>> Margulis wrote:
>> > Does anybody understand this behavior:
>> > node1-claudiom 63 % pwd
>> > /scratch/claudiom/111
>> > node1-claudiom 64 % ls
>> > topol.tpr
>> > node1-claudiom 65 % mdrun
>> > :-) G R O M A C S
>> > Segmentation fault
>> You could try running mdrun through strace, if the
>> latter is available on your
>> system. (It should be present on most Linux
>> To do this, use "strace mdrun", which will print a
>> list of the system calls
>> mdrun uses up to the point of the segmentation
>> fault. This might provide a
>> clue as to what it is trying to do. Since it crashes
>> pretty quickly, there
>> shouldn't be too many calls to sort through.
>> Happy holidays to all,
>> Lieven Buts
>> Department of Ultrastructure
>> Vrije Universiteit Brussel
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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