[gmx-users] is there any reasonable way to produce a custom topology?

[Maik Goette]

:)

I thought something similar.
I can't lose the impression, that many people think of simulating things 
as a totally easy way to get whatever they want.
And its clear, that all (free) tools can handle the 
"do-whatever-I-mean"-command...;)

Just feed the PDB and get out a 1µs sim of a 150kD protein...
BTW...simulating this and the catalytic reaction in the active site via 
QM totally automatically is a must-have, too. Any program, which can't 
handle this, is crap...I'm so sorry, that there seems to be no tool on 
the market which is that great and able to do, what I wish...:)

Sorry for the spam, guys...but I have the feeling, that these kind of 
questions grow and grow...

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Mark Abraham wrote:
> Yegor Isakov wrote:
> 
> You are much more likely to get a helpful response from the people who 
> know this software best (the programmers, who do read this list) if you 
> express a little less of your frustration, and imply less condemnation 
> of their software design choices, which you probably don't understand 
> yet anyway!
> 
> Check your assumptions - you haven't paid anybody for the right to rant 
> at them :-) You'd also do well to remember that GROMACS doesn't come 
> with a warranty of fitness for any purpose :-)
> 
>> I would be extremely pleased if anybody would tell me how could I foce 
>> that stupid pdb2gmx program to follow the path to the directory 
>> containing .itp files (~/share/top).
> 
> 
> Setting the environment variable GMXLIB makes various GROMACS utilities 
> look there instead of the default, which is probably 
> $GMXDATA/gromacs/top. GMXDATA gets set when you run GMXRC which is 
> installed in the same place as the GROMACS binaries. You may need to 
> link the existing contents of $GMXDATA/gromacs/top/ to ~/share/top/ in 
> order to have everything work, as I couldn't get GMXLIB to accept a path.
> 
> I note that the manual mentions GMXLIB only in passing in a few of the 
> programs' man pages, and not at all in the Appendix section on 
> Environment variables. Usage of GMXRC is also not mentioned in the 
> installation section on the web page. Can either of both of these be 
> looked at, please?
> 
>> Although in the manual it was recomended to avoid modifying .rtp 
>> files, that is the only way I found to produce a topology 
>> "semi-automatically." Is there any other  reasonable way to produce a 
>> topology? Is anywhere more intelegent converter of pdb files? Is 
>> anywhere a program that permits creating a stable bond between 2 
>> atoms  in a topolgy without blowing up the last one?
> 
> 
> Construction of topologies for MM calculations is a process that 
> involves making judgements. Automating "sensible" defaults is an 
> extremely tricky business, given the multiplicity of force fields, the 
> kinds of kludgey PDB files that you can get hit with, and the 
> innumerability of the molecules people will want to use. Then of course, 
> a default someone thinks is sensible, someone else will think is 
> ludicrous, and they might both be right for different applications. 
> Basically you will need to do some work yourself if you are doing 
> something new... big surprise.
> 
> The limitation on one bonded interaction type per atom pair is not 
> unreasonable. It probably stems from an implementation decision as much 
> as a design choice. No force fields I'm aware of need this kind of 
> thing. You can have a distance restraint and a bonded interaction, 
> however, or different types of bonded interaction.
> 
> Mark
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