Re: Cleaving and capping protein with autopsf leads to parameter errors upon running NAMD

From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed May 02 2018 - 00:23:22 CDT

Dear Jacob,
Given that your error message indicates an angle in which the same atom
participates twice (596-598-596), I suspect that something got pretty
messed up in your psf. Why are you adding the termini as separate patches
in autopsf? A better approach would be just to modify the chain definitions
so that the patches are applied as FIRST/LAST patches (as designed) instead
of as standard patches.
Best,
Peter

On Wed, May 2, 2018 at 1:14 AM, Jacob Usadi <jusadi_at_uchicago.edu> wrote:

> Hello!
>
> I am having a small problem with modifying an existing protein structure.
> How can we properly modify this structure? Is there something we are
> missing? I discuss the error, the corresponding part of the PDB, and the
> context below.
>
> - - - - -
> The current error take the following form. We get it when first running
> minimization on our protein:
> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CC OC CC (ATOMS 596 598
> 596)
> [0] Stack Traceback:
> - - - - -
> The corresponding part of the PDB is as follows:
> ATOM 593 HG21 VAL P 40 5.374 10.281 3.664 0.00 0.00 PP1
> ATOM 594 HG22 VAL P 40 5.663 11.171 5.246 0.00 0.00 PP1
> ATOM 595 HG23 VAL P 40 7.009 10.763 4.119 0.00 0.00 PP1
> ATOM 596 C VAL P 40 5.695 13.380 1.030 0.00 0.00 PP1
> ATOM 597 OT1 VAL P 40 6.455 13.756 0.499 0.00 0.00 PP1
> ATOM 598 OT2 VAL P 40 4.707 13.463 1.159 0.00 0.00 PP1
> ATOM 599 N ILE P 41 6.427 14.451 0.913 0.00 0.00 PP2
> ATOM 600 HT1 ILE P 41 6.201 14.708 1.853 0.00 0.00 PP2
> ATOM 601 HT2 ILE P 41 7.417 14.354 0.815 0.00 0.00 PP2
> ATOM 602 HT3 ILE P 41 5.975 13.591 0.676 0.00 0.00 PP2
> ATOM 603 CA ILE P 41 5.965 15.488 0.017 0.00 0.00 PP2
> ATOM 604 HA ILE P 41 4.924 15.602 0.066 0.00 0.00 PP2
> - - - - -
> As you can see, this error occurs at the point between the NTER and CTER
> of adjoining protein sections. The reason we have this area in the PDB is
> because we had a previously run protein that we now wish to "cleave" and to
> which we add termini. Thus, the two parts were previously a single protein.
> We have modified it to be two sections with caps.
>
> To add the termini, we simply patch the protein using autopsf.
> - - - - -
>
> Is there an error with how we are trying to do the cleavage? Is the
> problem simply a missing parameter file? If so, I am unsure what to do
> given that I believe we are including all standard ones.
>
> Thank you very much for reading. If there is any more information that
> would be useful, please ask.
>
> Have a great day,
> Jacob
>
>
>
> --
> Jacob Usadi
> University of Chicago '19
> Mathematics
>

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