VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Dec 24 2020 - 09:19:58 CST

No worries. Glad to hear that you worked it out.
Best,
Peter

On Thu, Dec 24, 2020 at 4:25 AM Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> I have now found the origin of the duplicated bonds/angles. I had pushed
> twice the "Apply patches" on the gui. Very sorry for wasting your time
> about this silly mistake
> francesco pietra
>
> ---------- Forwarded message ---------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Thu, Dec 24, 2020 at 8:03 AM
> Subject: Re: vmd-l: Fwd: Fake angles created by AutoPSF
> To: Peter Freddolino <petefred_at_umich.edu>
> Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>
>
> The high pH trimer was re-built from scratch, getting the same results.
>
> I used the gui, replacing the default parameters with
> toppar_water_ions.str
> top_all36_prot.rtf
> top_all36_prot.rtf
> top_all36_carb.rtf
> top_all36_lipid.rtf
>
> like I did with the low pH trimer.
> Then "Everything"... >Guess and split" ... "Create chains" (Segments were
> OK).... "Apply patches"
>
> francesco
>
> On Thu, Dec 24, 2020 at 3:35 AM Peter Freddolino <petefred_at_umich.edu>
> wrote:
>
>> Could you give a little more info on how you ran autopsf? GUI or command
>> line? Did you reset the psfgen environment between your first and second
>> targets? If you build the high pH trimer in a completely fresh vmd session,
>> do you still get the same problem?
>> Thanks,
>> Peter
>>
>> On Wed, Dec 23, 2020 at 10:34 AM Francesco Pietra <chiendarret_at_gmail.com>
>> wrote:
>>
>>> Sorry, VMD 1.9.1 should be read 1.9.3
>>> ---------- Forwarded message ---------
>>> From: Francesco Pietra <chiendarret_at_gmail.com>
>>> Date: Wed, Dec 23, 2020 at 3:52 PM
>>> Subject: Fake angles created by AutoPSF
>>> To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>>>
>>>
>>> Hello
>>> I am facing a puzzle with AutoPSF (VMD 1.9.1 linux).
>>>
>>> I have to closely related homotrimers, built from X-ray diffr data, with
>>> several S-S bonds.
>>>
>>> The homotrimer at low pH allowed building correct psf/pdb and MD, so
>>> that I
>>> did not check the psf of the other homotrimer, at high pH.
>>> With the latter, minimization of psf/pdf gave error for the subuinit of
>>> segn AP1
>>>
>>> UNABLE TO FIND ANGLE PARAMETERS FOR SM SM SM (ATOMS 380 2044 380)
>>> ATOM 380 SG CYS A 94 -9.311 -18.367 56.731 1.00 0.00
>>> AP1
>>>
>>> The reason is that the 380-2044 bond was created twice
>>> psf BONDS
>>> 380 2044 380 2044 380 377 381 375
>>>
>>> and the fake angle 380-2044-380 was also created
>>> psf ANGLES
>>> 380 2044 2041 380 2044 380 380 377 379
>>>
>>> These anomalies are repeated in the other two subunits.
>>>
>>> I examined the starting pdb finding no anomalies at the various CYS
>>> residues. I also checked the applied DISU, which looked like to be
>>> correct
>>>
>>> Thanks for advice on where to search the error
>>>
>>> francesco pietra
>>
>>