[gmx-users] Metal interactions with proteins
RAHUL SURESH
drrahulsuresh at gmail.com
Mon Nov 20 18:01:55 CET 2017
Dear Justin
On adding this to the rtp file I received the error "Atom in residue CU 1
was not found in rtp entry CU with 1 atoms
while sorting atoms". for the pdb2gmx command.
Also the warning state
* "Warning: Starting residue CU1 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 successfullyOpening
force field file
/usr/local/gromacs/share/gromacs/top/charmm36.ff/merged.arn"*
last line of my pdb
ATOM 318 OT1 ALA 42 3.874 5.988 0.286 0.00
0.00 O
ATOM 319 OT2 ALA 42 4.613 5.549 2.283 0.00
0.00 O
TER 320 ALA 42
TER
HETATM 321 CU 1 1.905 -0.009 -4.349 0.00
0.00 CU
END
On Mon, Nov 20, 2017 at 9:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 11/20/17 11:05 AM, RAHUL SURESH wrote:
>
>> 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.
>>
>
> Look at any other ion in the .rtp file and follow suit, something like:
>
> [ CU ]
> CU CU 2.000 0
>
> (I have no idea what atom type you're trying to use, but that's what
> should be in the second column - name, type, charge, charge group).
>
> -Justin
>
>
> 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
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
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>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>>>
>>>>>
>>>> --
>>> ==================================================
>>>
>>> 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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>>
>>
> --
> ==================================================
>
> 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
>
> * Please search the archive at http://www.gromacs.org/Support
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>
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>
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--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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