VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Apr 23 2013 - 16:22:47 CDT

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> 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> 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
>>
>
>
>