[gmx-users] GROMACS state-of-the-art setup (was Re: Intermolecular Distance Restraints)

[David]

On Sun, 2004-08-15 at 19:32, Warren DeLano wrote:
> Thanks for the help...pdb2gmx -merge works like a champ.
> 
> As far PyMOL goes, I'd like to get a better handle on what the state of the
> art is with respect to setting up GROMACS simulations.  I'm hoping someone
> can answer the following questions:
> 
> - Is there currently a way to restrain sub-portions of a system using a
> conceptual selection language (ala XPLOR/CNS/PyMOL), rather than atom
> identifiers?
No.

> 
> For example, in the past I've needed to do stuff like the following.
> 
> select ligand, chain A
> select protein, chain B
> 
> restrain_position (all)
> unrestrain_position (ligand)
> unrestrain_position (protein within 10 of ligand)
> restrain_position (protein///143-144/)
> 
> restrain_distance (ligand///5/N), (protein///123/O), 3.2
> restrain_distance (ligand///6/O), (protein///122/N), 3.2
> 
> in order to set up models where certain interactions or conformations are
> assumed/enforced from the get-go.  
> 
> The above isn't all that far from being doable with PyMOL by using Python to
> simple read, edit, and write posre.itp and disre.itp files, but is there
> already some other tool which can do this efficiently for GROMACS?
Yes, you can do such kind of atom selections using the make_ndx program
with simple logical operations such as AND and OR (&, | respectively),
probably except for the distance related bit. Whether that's a better
solution than doing it from with pymol I cannot judge.

> 
> - Is there an easy way to avoid renumbering of residues and chain
> identifiers?  or a way to correct the final output from GROMACS so that it
> matches the naming used in the input PDB?
Naming probably not (you know why...). You can however generate an 
index file with pdb2gmx -n that will give you back the atoms in the 
original order (which is, as you know, quasi-random in pdb files). Upon reading
a pdb file we store the original numbering etc. but this does get lost 
when doing simulations.

> Setup, analysis, and sharing of results is harder if you're constantly
> having to renumber systems, and especially when you're using fixed
> identifiers in atom selections as in the above examples.  PyMOL could
> probably handle the remapping automatically stored the original identifiers
> in Python dicts, but perhaps there is already a simple solution to this
> problem?
> 
> - Is there any GROMACS tool for automatically assigning semi-reasonable
> charges and types to arbitrary organic molecules?  
No.

> 
> I'm not talking about QM-quality parmeterizations, but rather the quick and
> dirty (yes, mostly bogus) stuff that industrial computational chemists need
> to do on a routine basis in order to rapidly generate crude models of
> protein/ligand complexes.  PyMOL has a chemical substructure pattern
> recognition module that could be useful for this...

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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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