[gmx-users] Topology builder

Erik Lindahl lindahl at cbr.su.se
Wed Jul 4 16:10:14 CEST 2007


There are a couple of programs out there (e.g. Macromodel) that tries  
to do this, even for OPLS, but they fail miserably way too  
frequently. I've even seen cases where the autogenerated topology was  
reported as "likely high quality", but the small molecule didn't even  
have unit charge and the atom types were simply not correct.

Having said that, this functionality is implemented in the x2top  
tool, but you might need to extend the databases and/or hack it a  
bit.  If you really want to do it without even checking the  
topologies I would prefer a simpler forcefield like Gromos96 over  
OPLS, though (fewer atom types mean less errors).



On Jul 4, 2007, at 3:57 PM, Mark Abraham wrote:

>> Dear Mark,
>> The problem is a little bit more complicated. I want to build  
>> topologies
>> for
>> dozens of non-peptide inhibitor prototypes using OPLS FF. Thus, if  
>> there
>> is a
>> way to build this by an automatic procedure it would save much time.
> Well, if there was one, I might have mentioned it before :-)
> The difficulty is that assignment of atom type to arbitrary chemical
> species is a tricky pattern-recognition problem. Still, this must be
> something that programs like Autodock have to deal with, so you should
> have a look at such docking programs and see what they do.
> Otherwise, you could write such a program... :-)
> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list