[gmx-users] Re: OPLS-AA/L force field

you zou zou.you at live.com
Wed May 19 17:59:53 CEST 2010

Hi again,  Sorry I confused you with my question. My question is How can I make .gro file and .top file from drug.pdb (that removed from drug-enzyme.pdb)? If I can use x2top command I will make .top file just, is it true? I think .gro file is dependent on forcefiled too so If I use editconf command I will miss something, is it true?Thank you again
you zou wrote:
> Hi Justin,
> 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 bonds
> Can not find forcefield for atom C4-4 with 2 bonds
> ...
> Program x2top, VERSION 4.0.5
> Source code file: x2top.c, line: 207
> Fatal error:
> Could only find a forcefield type for 6 out of 24 atoms"

Not all of your atom types are described by ffoplsaa.n2t so you will have to add 
them. There are only a limited number of types that are covered by default.


> 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?

Do you just need a .gro file, and not a .top? My understanding from your first 
message was that you needed a topology. If you just need a .gro, then simply 
pass your .pdb file to editconf.


> 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 
> Gromacs manual.

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