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

[Justin A. Lemkul]

you zou wrote:
> Hi,
> 
> Thank you for your help.Now there is this question that I have just .pdb file
> and when use protonate command it is" protonate -f drg.pdb -o drg.gro", this
> is without hydrogens atoms too.
> 
> I think something is wrong, but I don't know what it is.In definition of
> "protonate" there is "protonate reads (a) conformation(s) and adds all
> missing hydrogens as defined in ffgmx2.hdb
> <http://rocks5.vki.ac.be/gromacs/online/hdb.html>." but I can't add
> hydrogens. What is my problem?
> 

Well, your command isn't correct.  The protonate command takes (at minimum) the 
-s flag, not -f (which is optional, and context-dependent, if I recall).

The other fact is that if a residue isn't listed in ffgmx2.hdb, it won't get 
protonated, but it is trivial to add new molecules into the .hdb file with the 
help of the manual.  The syntax for .hdb entries is straightforward.

-Justin

> Thanks
> 
> you zou wrote:
>> Hi again,
>> 
>> Sorry, I have one question now, what is the meaning of structure? I think 
>> coordinates is structure, is it true?
>> 
> 
> Yes, a coordinate file contains a structure.
> 
>> 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?
>> 
> 
> The underlying assumption when running any simulation is that you have
> developed the proper parameters for the ligand and that it has an appropriate
> structure. If you need additional hydrogens, the Gromacs "protonate" tool can
> generate an all-atom structure.
> 
> -Justin
> 
>> 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 f
> orcefield type for 6 out of 24 atoms"
>>>> 
>>> 
>>> Not all of your atom types are described by ffop
> lsaa.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<
> br>>>
>>>> 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
>>>>> 
>> & gt;>> 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 c
> an 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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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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