[gmx-users] Metal interactions with proteins

[RAHUL SURESH]

Dear Justin

Why is there no aminoacids.rtp file in charmm36ff?
As mentioned before I have added the metal ion parameters in nonbonded.itp,
ions.ipt and atomtypes.itp. While performing simulation using the command *"gmx
pdb2gmx -f cu.pdb -o cu.gro -p cu.top" *I receive the following error

"Residue 'Cu' not found in residue topology database"

There describe a note* "*

*Warning: Starting residue Cu43 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues. This chain
does not appear to contain a recognized chain molecule. If this is
incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8
lines of specbond.dat converted successfully".*
How do i debug this?





On Thu, Nov 16, 2017 at 8:26 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
wrote:

> That’s good enough  to perform the simulation. Thank you Justin.
>
>
>
> On Thu, 16 Nov 2017 at 6:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 11/16/17 4:12 AM, RAHUL SURESH wrote:
>> > On Wed, Nov 15, 2017 at 6:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> >
>> >>
>> >> On 11/15/17 6:44 AM, RAHUL SURESH wrote:
>> >>
>> >>> Hello users
>> >>>
>> >>> I am performing Metal-protein interactions with Charmm36ff using
>> gromacs.
>> >>> The metals under study are Cu and Ag in +2 state. Is it sufficient to
>> add
>> >>> the topology,i.e the necessary parameters (LJ-potentials) in
>> nonbonded.itp
>> >>> and ions.itp alone?
>> >>>
>> >> Yes (unless you want pdb2gmx to deal with them, in which case they
>> need to
>> >> be defined in atomtypes.atp, as well). Whether or not those parameters
>> are
>> >> a suitable model of reality is another matter (no classical MD force
>> field
>> >> treats transition metals particularly well).
>> >>
>> > Thank you for the clarification. I will add it in atomtypes too.
>> >
>> >> In case of nonbonded.itp file, i find charge for most atom types are
>> >>> mentioned to be 0.000 and in the line
>> >>> *" ; Updated Mg2+ parameters by Allner et al. (DOI:
>> 10.1021/ct3000734)MGA
>> >>> 12      24.305000    0.000  A   0.277000    0.01234280 " *the charge
>> for
>> >>> this ion is also mentioned to be 0.000 and atom type is refered as
>> MG*A.
>> >>> *What
>> >>> does this MGA refers to and why is the charge 0 for this ions.
>> >>>
>> >> MGA is the atom type for Mg2+ with the parameters by Allner et al. in
>> the
>> >> linked paper. We have to distinguish between that Mg2+ type and the
>> >> official, "standard" Mg2+ CHARMM36 ion type.
>> >>
>> > By default do charmm36 have every metal ions?
>>
>> If you don't see it in the provided files, it's not there.
>>
>> > In case I have to add the topology for Cu2+ and Ag2+, how can I name the
>> > atom type?
>>
>> However you like.
>>
>> > Should the charge be 0.000? In such case when we mention the charge to
>> be
>> > zero, won't it denote just the atom instead resembling the ion?
>>
>> Again, the charge in ffnonbonded.itp is completely irrelevant. The
>> actual charge is read either from an .rtp entry (if processed by
>> pdb2gmx) or ions.itp (if added e.g. by genion).
>>
>> > I crosschecked with that of oplsaaff.. There in the nonbonded terms,
>> every
>> > atom is given some partial charges.
>>
>> ...which are never used. It's confusing, I know. We should probably do a
>> big cleanup of ffnonbonded.itp and remove unused columns.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
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> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>



-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*