[gmx-users] Metal interactions with proteins
Justin Lemkul
jalemkul at vt.edu
Mon Nov 20 18:33:36 CET 2017
On 11/20/17 12:01 PM, RAHUL SURESH wrote:
> 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
The line for the Cu ion is incorrectly formatted; you need both the
residue name and atom name on that line.
-Justin
>
>
>
>
> 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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>>>>>>
>>>>>>
>>>>>>
>>>>> --
>>>> ==================================================
>>>>
>>>> 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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>>>>
>>>
>> --
>> ==================================================
>>
>> 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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>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
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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
==================================================
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