VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Dec 24 2020 - 03:24:44 CST

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
>
>