Re: Re: problems mutating HID to TYR for free energy calculations

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Mar 08 2017 - 09:45:49 CST

Are ANY coordinates assigned? Your pdb may not match the resname/resid
of the segment generated, leading to everything being filled by 0. If
there aren't any adjacent assigned coordinates, psfgen can't guess the
coordinates for the next atom in the sequence.

-Josh

On 03/07/2017 04:43 PM, Nehad Elsalamouny wrote:
> 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
>
>
>

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:08 CST