[gmx-users] Re: OPLS-AA/L force field
zou.you at live.com
Wed May 19 09:02:55 CEST 2010
Thank you for your help, But when I run x2top command there is one error that is:"Can not find forcefield for atom C1-1 with 2 bondsCan not find forcefield for atom C4-4 with 2 bonds...Program x2top, VERSION 4.0.5Source code file: x2top.c, line: 207Fatal error:Could only find a forcefield type for 6 out of 24 atoms"I don't know how can I adjust this error.I have one more question again, this command give me a top file, if I want gro file of this pdb (drug that has removed from drug-enzyme complex) how can I do that?
you zou wrote:
> Dear Users,
> I have one question about Drug-Enzyme Complex,Similar to tutorial If I
> want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug
> but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg
> Beta version" server too, or not?
No. You can't use two different force fields in one simulation system.
> If I can't use this server, how can I make .gro file and .itp file for
> drug that remove from initial .pdb file?
There are several programs in the User Contributions from the website, x2top
(which is distributed with Gromacs), or you can build the topology by hand. No
matter what you choose, you need a thorough understanding of the mechanics of
your chosen force field, methods of validation, and of course Chapter 5 in the
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