Buried in the output, though no unknown atoms were reported:
(Residue 15: DHU, Nonterminal, was not found in name map.)
(Residue 16: DHU, Nonterminal, was not found in name map.)
(Residue 45: 7MG, Nonterminal, was not found in name map.)
It looks like the parameter checking didn't look for dihedrals? Seems
'check' should have found the problem before you solvated and added ions.
My best guess is that you have hit a bug in leap, possibly due to
oddness in your pdb. But you still may need those torsion terms.
Bill
On 4/27/16 11:29 PM, Prayagraj Fandilolu wrote:
> Hello Sir,
>
>
> I am using PDB 1EHZ with all its modified bases. I am sourcing ff99bsc0
> before sourcing leaprc.modrna08
>
> I am using xleap from ambertools15.
>
>
> To find out the problem I have tried the subsets of pdb and I found the
> problem in 7MG residue. The dihedral missing is here in the residue..
>
>
> For more details and command syntax I am attaching the .log file for your
> reference.
>
>
> I will be highly obliged if I could know what should be my next steps to
> solve the issue??
>
>
> Thanks in advance…
>
> Prayagraj Fandilolu
> Research Scholar,
> Structural Bioinformatics Unit
> Department of Biochemistry
> Shivaji University, Kolhapur - 416004
> (MS) India
>
> On Mon, Apr 25, 2016 at 6:03 AM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Sun, Apr 24, 2016, Prayagraj Fandilolu wrote:
>>> **No torsion terms for CB-N*-CR-H5
>>>
>>> I am using parameters from leaprc.modrna08 with ff99bsc0.
>> Please post the *exact* commands you gave to tleap. It would also help
>> if you gave us the PDB id you are using. What version of amber? Are you
>> following the instructions at the top of the leaprc.modrna08 file?
>>
>> Do you have modified RNA bases? If so, please try different subsets of
>> the pdb file to see if the problem is related to the modified bases, or
>> not. Trying to find a minimal PBB file that shows the error would be a
>> good first step.
>>
>> ....dac
>>
>>
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Received on Thu Apr 28 2016 - 01:30:04 PDT
