VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Apr 23 2013 - 17:49:23 CDT

Hi Peter,

If you are using mutator to prepare a FEP simulation, the three letter
code won't be ASN. For FEP calculations, you want a single residue that
has both side chains present, and to alert the user to this fact, the
residues are given names using the one letter amino acid codes with a 2
indicating the direction of mutation. V2N is actually expected if you
happen to be mutating a Valine to an Asparagine, which should look
almost identical to ASN except for a methyl hanging off the mutated
residue. Since you intended to mutate a ASP to ASN, the expected resname
is actually D2N, which to me suggests you may have accidentally picked
out the wrong residue for mutation? If your protein has multiple
segments, you should also specify the proper segment name in the mutator
window (ie. if the ASP you wanted to mutate was on segment P3 and resid
423, you'd specify the residue as P3:423 in the mutator GUI), and is my
best guess as to why you are seeing unexpected results.

-Josh

On 04/23/2013 04:22 PM, Ajasja Ljubetič wrote:
> Usually it's considered good form to keep the mailing list in the CC.
>
> I am afraid I can't help you of the top of my head. Here are some
> generic tips:
>
> * Are you using the latest VMD version?
> * Is the problem repeatable if you restart your computer
> * Is the problem specific just for your current 3D structure or for
> any 3D structure? (so have you tried with another pdb/psf pair?)
>
>
> HTH,
> Ajasja
>
>
> On 23 April 2013 22:12, Peter Murphy <pwmurphy_at_dal.ca
> <mailto:pwmurphy_at_dal.ca>> wrote:
>
> I selected the pdb and PSF files, put in the residue # and the
> three letter code to mutate to ASN. In addition I am using FEP.
> Not getting any error messages, the plugin says its completed fine.
>
> Other than that, not really anything else I can provide except the
> input and output files (and I can if that would help).
>
> Thanks for your fast response... I appreciate it!!
>
> Peter
>
>
> On 23/04/2013 4:29 PM, Ajasja Ljubetič wrote:
>> Yes, I have two ideas:
>>
>> a) Describe exactly what you have done (with warning and error
>> message) as there is not enough info in your question to help you.
>> b) delete the surplus atoms of ASP (the oxygen and the proton),
>> rename the residue to ASN and rebuild using psfgen.
>>
>> HTH,
>> Ajasja
>>
>>
>> On 23 April 2013 20:40, Peter Murphy <pwmurphy_at_dal.ca
>> <mailto:pwmurphy_at_dal.ca>> wrote:
>>
>> Hello everyone,
>>
>> I am trying to figure out what's going on with the
>> mutator plugin. I've used it successfully many times before
>> (mostly for mutating to Trp), but seem to be running into
>> problems this time around when trying to mutate to ASN.
>> Instead of mutating ASP to ASN, it is giving my V2N?? When I
>> turn on a CPK representation of the residue post mutation
>> (V2N) it appears the V2N residue matches the structure of ASN
>> almost exactly....
>>
>> I've run out of ideas... anyone have any thoughts?
>>
>> Thanks in advance,
>>
>> Peter
>> --
>> Ph.D Candidate,
>> Dalhousie University
>> Halifax, NS
>> Canada
>>
>>
>
>