VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Dec 23 2020 - 20:35:40 CST

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