[gmx-users] Metal interactions with proteins

[Justin Lemkul]

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
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> 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

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