[gmx-users] Metal interactions with proteins

[RAHUL SURESH]

Dear Justin

Sorry for the inconvenience. Tried every possible way and couldn't find any
proper way to add datas into merged.rtp. As you have suggested, Yes i have
made some incorrect format entry.
Can you please guide me to make a valid entry in rtp file? Which one is the
right format. I have searched web over the best of my knowledge and
couldn't find any valuable ideas.

Please help me in this.

Thanks in advance.

On Fri, Nov 17, 2017 at 7:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/17/17 2:30 AM, RAHUL SURESH wrote:
>
>> 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*
>>
>
> This appears to indicate an incorrectly formatted .rtp entry.
>
> 2. I added TER in the pdb file and still the same error. Then I removed Cu
>> from merged.rtp and again error prevails.
>>
>
> pdb2gmx can't process any residue not properly entered into the .rtp file,
> so if you removed it, naturally you're going to get an error. Solve problem
> (1) before doing anything else.
>
> -Justin
>
>
>>
>>
>> *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
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==================================================
>>>
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>>>
>>
>>
> --
> ==================================================
>
> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*