[gmx-users] protein-SWCNT md simulation

[Justin Lemkul]

On 2/3/13 8:20 AM, Atila Petrosian wrote:
> Dear gromacs users
>
> I'd like to study the interaction between carbon nanotube and a protein.
> I used amber03 parameters for both protein and cnt.
>
> I have made cnt.top for the nanotube by g_x2top and pr.top for protein by
> pdb2gmx.
>
> I made adjustments to cnt.top to become cnt.itp file to be #included in
> pr.top file.
>
> My cnt.top file is as follows:
>
>
> ; Include forcefield parameters
> #include "./cnt.ff/forcefield.itp"
>
> [ moleculetype ]
> ; Name            nrexcl
> cnt                 3
>
> [ atoms ]
> .
> .
> .
> [ bonds ]
> .
> .
> .
> [ pairs ]
> .
> .
> .
> [ angles ]
> .
> .
> .
> [ dihedrals ]
> .
> .
> .
>
> [ system ]
> ; Name
> cnt
>
> [ molecules ]
> ; Compound        #mols
> cnt                 1
>
> For creation the cnt.itp from cnt.top file, I deleted
>
> ; Include forcefield parameters
> #include "./cnt.ff/forcefield.itp"
>
> *** and ***
>
> [ system ]
> ; Name
> cnt
>
> [ molecules ]
> ; Compound        #mols
> cnt                 1
>
> -----------------------------------
>
> Then I added
>
> ; Include forcefield parameters
> #include "./cnt.ff/forcefield.itp"
>
> to the pr.top file so that first lines of pr.top are as follows:
>
> ; Include forcefield parameters
> #include "amber03.ff/forcefield.itp"
> #include "./cnt.ff/forcefield.itp"
>

Given the information you posted in your other message, this can't work.  You're 
specifying two force fields and hoping they will work together.  You need one, 
unified force field that adequately describes all elements of your system. 
Mixing and matching is a recipe for disaster.

>
> and the end of pr.top file is as follows:
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include cnt topology
> #include "cnt.itp"
>
> ; Include water topology
> #include "amber03.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
>
> ; Include topology for ions
> #include "amber03.ff/ions.itp"
>
> [ system ]
> ; Name
> Protein-cnt complex
>
> [ molecules ]
> ; Compound        #mols
> Protein             1
> cnt                 1
>
>
> When I use grompp grompp -f em.mdp -c pr_cnt.gro -p pr.top -o em.tpr,
>
> grompp give me the following error message:
>
>
> WARNING 1 [file forcefield.itp, line 1]:
>    Too few gb parameters for type
> ********************************************
>
> Couldn't find topology match for atomtype
> Aborted
>
>
>
> Is my manner true?
>

No, see above.

> How to resolve this problem?
>

Use a single force field, and if you're running an implicit solvent simulation, 
be sure that all of the atomtypes have all the necessary parameters for doing so.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
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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