[gmx-users] Metal interactions with proteins

[RAHUL SURESH]

Dear Justin

I have tried various measures to over come it.

1. I added Cu in merged.rtp and still the error prevails.





*Error: Fatal error:in .rtp file in residue ions at line:        Cu*
2. I added TER in the pdb file and still the same error. Then I removed Cu
from merged.rtp and again error prevails.




*Error: Fatal error:Residue 'Cu' not found in residue topology database*
last few lines of my pdb




*ATOM    319  OT2 ALA    42       4.613   5.549   2.283  0.00
0.00           O  TER     320      ALA    42 ATOM    321      Cu
0       1.905  -0.009  -4.349  0.00  0.00          Cu  END*

I changed Cu atom number to 43 and also 1 but no use.
I added addition TER after 320 then again the error remains.

Please help me.


On Fri, Nov 17, 2017 at 1:42 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/16/17 1:53 PM, RAHUL SURESH wrote:
>
>> Dear Justin
>>
>> Why is there no aminoacids.rtp file in charmm36ff?
>>
>
> Because the way the CHARMM topology and parameter files are constructed
> makes it nearly impossible to actually write out only certain types of
> molecules, we lumped (almost) everything into one file called "merged.rtp."
> The only exception is the nucleic acid files, which are separate (again, by
> necessity due to how CHARMM works).
>
> 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?
>>
>
> It appears pdb2gmx is interpreting your Cu ion as part of the same chain
> as a protein. Separate it using TER or a different chain identifier so that
> pdb2gmx doesn't try to make it some kind of terminus.
>
>
> -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
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>
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*