Re: problems mutating HID to TYR for free energy calculations

From: Nehad Elsalamouny (nehade_at_uow.edu.au)
Date: Tue Mar 07 2017 - 17:39:37 CST

   I am really sorry. Unfortunately, this didnít fix the problem. Still unable to guess the coordinates.
   This is part of the error messages i receive:
    
    psfgen) Warning: failed to guess coordinate due to bad angle CB CG HG
    psfgen) Warning: failed to guess coordinate due to bad angle CD CG HG2
    psfgen) Warning: failed to guess coordinate due to bad angle CB CG HG
    psfgen) Warning: failed to guess coordinate due to bad angle CB CG HG
    psfgen) Warning: failed to guess coordinate due to bad angle CB CG HG

Thanks

Nehad
> On 8 Mar 2017, at 10:02 AM, Brian Radak <bradak_at_anl.gov> wrote:
>
> You still need a generate command for the bonds. You should have the following in your script:
>
> segment H2Y {
> pdb xxxxx.pdb
> auto angles dihedrals
> }
> coordpdb xxxx.pdb H2Y
> guesscoord
>
> On 03/07/2017 05:50 PM, Nehad Elsalamouny wrote:
>> Hi Brian,
>>
>> Thanks for your email. Here you will find the rtf file attached. I thought the problem might be in the IC too. I rechecked them they are correct! Do you think it is something missing in psfgen script itself?
>>
>> kind regards,
>>
>> Nehad.
>>
>>
>
> --
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak_at_anl.gov

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