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

From: Jacob Usadi (jusadi_at_uchicago.edu)
Date: Wed May 02 2018 - 00:14:40 CDT

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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