[gmx-users] Metal interactions with proteins
drrahulsuresh at gmail.com
Fri Nov 17 08:30:39 CET 2017
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*
2. I added TER in the pdb file and still the same error. Then I removed Cu
from merged.rtp and again error prevails.
*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
>> 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
>> 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
>> 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 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
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