quot; mention in it is because
it's preferable to do this with a centered protein. It then tells you the
best places to replace oxygens from water with positive ions; you can then
translate the PDB file back into gromacs format (ideally after adding
hydrogens again with something
(15, "P", "phosphorus", 1.80, 1.80, 1.10, "pink", 0);
insert(16, "S", "sulfur", 1.80, 1.90, 1.04, "yellow",
ACCEPTOR_ATOM);
insert(33, "As", "arsnic", 2.00, 2.10, 1.21, "
In message <[EMAIL PROTECTED]> (on 3
October 2007 19:09:54 -0400), [EMAIL PROTECTED] (Allen Smith)
wrote:
>In message <[EMAIL PROTECTED]> (on 4 October 2007 04:04:05 +1000),
>[EMAIL PROTECTED] (Mark Abraham) wrote:
>>Allen Smith wrote:
>>> Umm... the atom numbers
t you're doing is fine, until you go to change the recipe, which is
>> > what you're trying to do here. :-)
>> >
>> > Mark
>> >
>> >
>> > --
>> >
>> > Message: 7
>> > Date: Thu
In message <[EMAIL PROTECTED]> (on 4 October 2007 04:04:05 +1000),
[EMAIL PROTECTED] (Mark Abraham) wrote:
>Allen Smith wrote:
>> In message <[EMAIL PROTECTED]> (on
>> 3 October 2007 19:13:51 +0200), [EMAIL PROTECTED] (maria goranovic)
>> wrote:
>>> Hi,
want more solvent added, don't use genbox. The question will be
how to do this while making sure you don't have any vacuum spaces.
-Allen
--
Allen Smith http://cesario.rutgers.edu/easmith/
There is only one sound argument for democracy, and that is the arg
- for instance, people doing real NMR
restraints may not want the changes that I've had to do for purposes of
using NMR restraints for homology modeling, since they involve expansion of
arrays (to allow for more restraints per atom) that might be problematic
with lots and lots of
he COM motion removal (e.g., if rotation of the rest of the
system to cancel out center-of-mass motion might do something like leaving
the frozen part behind).
-Allen
--
Allen Smith http://cesario.rutgers.edu/easmith/
There is only one sound argument for democra
idue.
>
>I hope this does make sense and provides at least one reason to implement
>such a procedure.
>
>Marc
>--
> Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
> mailto:[11]baaden at smplinux.de - [12]http://www.baaden.ibpc.fr
least for layers other than the _very_ outermost one.
Thanks,
-Allen
--
Allen Smith http://cesario.rutgers.edu/easmith/
February 1, 2003 Space Shuttle Columbia
Ad Astra Per Aspera To The Stars Through
In message <[EMAIL PROTECTED]> (on 13
August 2007 17:12:41 -0400), [EMAIL PROTECTED] (Allen Smith)
wrote:
>
>A build on IRIX 6.5.30m with cc version 7.3.1.3m, using -n32 -mips4, gives
>the following error:
>
>checking floating-point format... configure: WARNING: Unknown fl
nd putting this result into the message
about an "Unknown floating-point format" for any future encountering of this
problem - not something I have time to do...) may be of interest.
Thanks,
-Allen
--
Allen Smith http://cesario.rutgers.edu/easmith
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