[gmx-users] Metal interactions with proteins

Mon Nov 20 17:13:42 CET 2017

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
>>>>
>>>> ==================================================
>>>>
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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
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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

==================================================