[gmx-users] Vdwradii.dat uses (was Re: g_sas Vdwradii.dat)

(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, "

Re: [gmx-users] to add counter ions based on potential

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

[gmx-users] configure: Unknown floating-point format w/IRIX?

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

Re: [gmx-users] configure: Unknown floating-point format w/IRIX?

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

[gmx-users] Freeze groups and rotation

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

Re: [gmx-users] how to calculate internal energy for energygroups?

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

Re: [gmx-users] frozen group, pull code and COM motion removal

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

Patchfile? Re: [gmx-users] gromacs 3.3.2

- 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

Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready

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

Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready

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,

Re: [gmx-users] Re: getting a good .gro file from a pdb file while thetopology is ready

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

Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready

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