[gmx-users] help with chromophore of a GFP

[Justin Lemkul]

On Wed, Mar 20, 2013 at 1:01 PM, Anna MARABOTTI <amarabotti at unisa.it> wrote:

>
>
> Dear gmx-users,
>
> it's about two weeks that I'm trying to solve this
> problem, and I can't, so I'm asking your help.
>
> I want to do some MD
> simulations on a protein of the family of green fluorescent protein.
> This protein, as you know, has a chromophore (CFY) derived from four
> residues of the protein (F64-C65-Y66-G67) and covalently bound to the
> rest of the protein chain. How to parametrize this object, since it is
> not recognized by pdb2gmx? I looked at the gmx-users list and the
> suggestion was to create a new entry in the .rtp file of the selected
> forcefield. I decided to use Amber99SB since it seemed the better for my
> scope, then I start trying to parameterize it. This is what I did:
>
>         *
>
>
> I used Pymol to add H to my pdb file, since I want to use an all H
> forcefield and since Antechamber (see below) does not work without H
>         *
>
>
> I extracted the segment V63-CFY-H68 from my .pdb file. I did this
> since, when I extracted CFY only, I had problems with the terminals
>         *
>
>
> Following the Antechamber tutorial, I used Antechamber (using the
> traditional Amber force field, not GAFF) to calculate charges and to
> assign atom types to this segment.
>         *
>
> I used these calculated
> parameters in order to add the CFY residue to aminoacids.rtp in
> amber99sb.ff directory.
>         *
>
> I tried to modify also aminoacids.hdb, but
> since it seemed too complicated to me, I decided to keep it unchanged,
> and to give pdb2gmx the protein with H already present
>         *
>
> No need to
> add new atom/bond types to ffbonded.itp and ffnonbonded.itp: they seem
> all present. Since CFY is bound to the rest of protein with common
> peptide bonds, I did not change specbond.dat either.
>         *
>
> I added CFY
> in residuetypes.dat with the specification "Protein"
>
> In my opinion,
> all was ready to go, instead...
>
> When I launched pdb2gmx to my protein
> with H added by PyMol, I got immediately an error:
>
> Fatal error:
>
> Atom
> H01 in residue SER 3 was not found in rtp entry NSER with 13 atoms
>
>
> while sorting atoms.
>
> For a hydrogen, this can be a different
> protonation state, or it
>
> might have had a different number in the PDB
> file and was rebuilt
>
> (it might for instance have been H3, and we only
> expected H1 & H2).
>
> Note that hydrogens might have been added to the
> entry for the N-terminus.
>
> Remove this hydrogen or choose a different
> protonation state to solve it.
>
> Option -ignh will ignore all hydrogens
> in the input.
>
> For more information and tips for troubleshooting,
> please check the GROMACS
>
> website at
> http://www.gromacs.org/Documentation/Errors [1]
>
> >From this error I
> understand that:
>
>         *
>
> the code for H in PyMol is different from the
> code for H in Amber (read from aminoacids.rtp); in order to correct this
> error, I should add -ignh in order to ignore H in input.
>         *
>
> If I add
> -ignh, all the H of CFY will be ignored too, and I will not be able to
> add them since I did not modify aminoacids.hdb
>         *
>
> since I made
> calculations on CFY with H added by PyMol, probably also my codes for H
> will be wrong.
>         *
>
> If I use "reduce" (the Amber tool to add H, as
> suggested by the tutorial) to add H to my protein, it does not add H to
> CFY because it complaints that the residue is not in HETATM connection
> database (but the record CONECT is present in .pdb file). If I add H to
> CFY alone, I have problems with the terminals.
>
> My question is,
> obviously: how can I parameterize this chromophore correctly? Please
> give me, if possible, some step-by-step indications on what to do. I
> made dozens of trials, ALL with errors, and I really do not know how to
> do.
>
>
There are parameters published for the GFP chromophore under the CHARMM
force field; is there some reason those are unsuitable?  No need to
reinvent the wheel.  With the published parameters, one simply needs to
create an .rtp entry and pdb2gmx runs fine, no need to mess with
antechamber, PyMOL, etc.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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