[gmx-users] Re: Re: problems running grompp with protein-ligand complex

[Justin A. Lemkul]

Ragnarok sdf wrote:
> I am working with a system using ffamber99 forcefield and trying to
> set up a ligand protein complex system. I have encountered some
> problems with grompp now.
> In my past email, the problem was that : > Fatal error: Found a second
> defaults directive, file "ligand.itp", line 5. Then the following
> solution was given:
> 
> " You have to combine all atomtypes into one file something like
> 
> filename ff_atomtypes.itp
> 
> #define FF_ATOMTYPES
> 
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> 1               2               yes             0.5     0.8333
> 
> 
> [ atomtypes ]
> ; name        mass      charge    ptype               sigma
> epsilon
> 
>      S       0.0000  0.0000  A   3.56359e-01  1.04600e+00
>    CC      0.0000  0.0000  A   3.39967e-01  3.59824e-01
>    HO      0.0000  0.0000  A   0.00000e+00  0.00000e+00
>    N3      0.0000  0.0000  A   3.25000e-01  7.11280e-01
> all atom types from amber force field 99 and also from your ligand (check if
> parameters are ok).
> 
> 
> delete atomtypes and defaults entry in your ligand.itp
> 
> load in your .top
> 
> #include "ff_atomtypes.itp"
> 
> #include "receptor.itp"
> #include "ligand.itp"
> "
> I tried to do this and ended up with the following .top file:
> 
> ; 15d-pgj2_GMX.top created by acpypi on Wed Dec  3 14:10:55 2008
> 
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> 1               2               yes             0.5     0.8333
> 
> ; Include 15d-pgj2_GMX.itp topology
> #include "15d-pgj2_GMX.itp"
> 
> [ system ]
>  15d-pgj2
> 
> [ molecules ]
> ; Compound        nmols
>  15d-pgj2         1
> 
> And all the atomtypes are in the 15d-pgj2_GMX.itp, which is too big to
> put here. But is present in past posts.
> Ok, so no grompp tells me the same error it did before. Fatal error:
> Found a second defaults directive, file "15d-pgj2_GMX.top"
> 

I would suggest a thorough read through Chapter 5 in the manual to understand 
topology structure.  Also have a look at normal protein topologies and all the 
files for the standard force fields (*bon.itp, *nb.itp, *.atp, etc.).

What you've got in your topology is a [ defaults ] section that typically 
belongs in the top-level #included force field file (see, for example, the 
contents of ffamber99.itp if you are interested in the AMBER force fields).  If 
that [ defaults ] section is in 15d-pgj2_GMX.itp as well, then you're calling it 
twice, since it is in the .top twice.

> When I substitute the 15d-pgj2_GMX.top for the 15d-pgj2_GMX.itp in my
> protein.top grompp gives out the following error:
> 

A .top within a .top?  That sounds like a mess.

> Fatal error:No such moleculetype PJ2
> 

Based on your description of what you've done, I'm still confused.  What is in 
15d-pgj2_GMX.top versus 15d-pgj2_GMX.itp?  Does this file define the molecule 
PJ2?  Or does it contain the [ defaults ] and [ atomtypes ] that you've shown 
above.  If you can provide a concise list of what is contained within all your 
files, you'll get better advice :)

Bottom line is the contents of your .top do not actually define your molecule, 
so you've got a huge chunk of information missing.  You need a simple .itp file 
for your ligand that contains the [ moleculetype ] information (again, see Ch. 
5) and nothing else - no atomtypes, defaults, or other stuff that's supposed to 
be in the force field already.

-Justin

> Now I am quite confused and would like some advice on the matter.
> Thank you
> Fabrício Bracht
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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