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

[you zou]

Hi again,Sorry, I have one question now, what is the meaning of structure? I think coordinates is structure, is it true?If it is true, when I used "editconf -f drg.pdb -o drg.gro" number of atoms are different from top file and editconf can not add hydrogens to drg.gro. If Gromacs can handle .pdb, How can it do this, because number of atoms are different(Which command I have to use?). If can't handle it how can I add Hydrogens to drg.gro?Thanks,

you zou wrote:
> 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?

If you want to use x2top, the assumption is that the structure is already 
appropriate as is, that is it is properly protonated. The only tool that is 
smart enough to add force field-specific hydrogens is pdb2gmx. If you're using 
OPLS-AA, then you should have all hydrogens present, anyway. If that's true, 
then you can use editconf to create a .gro file (which is not absolutely 
necessary; Gromacs can handle .pdb files just fine). If you don't have all the 
appropriate atoms present in your molecule's structure, then you need to build a 
proper structure.

-Justin

> 
> 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 ...
> &g t; 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.
> 
> http://www.gromacs.org/Documentation/File_Formats/.n2t_File
> 
>> 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 topo logy. If you just need a .gro, then
> simply pass your .pdb file to editconf.
> 
> -Justin
> 
>> 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 ne
> ed 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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