CT1 terminal patch for THR

From: GONZALEZ NOYA, EVA (eva.noya_at_iqfr.csic.es)
Date: Mon Mar 07 2011 - 14:47:57 CST

Hi everyone,

I am trying to put a CT1 patch at the c-terminal of a protein whose last residue is THR. However when I try to do that I get an error message when running NAMD

UNABLE TO FIND ANGLE PARAMETERS FOR CD CT1 CT1

I saw an old post where some people got into a similar problem but in that case the last residue was GLY.

At that time the suggestion was to use a modification of patch CT1 where as far as I've seen only involved a change in the charges (although I do not know which criterium was used to decide the new charges).

I saw that simply removing the angle that NAMD is complaining about from the psf file, the problem seem to be solved. However I do not know if this is introducing some error in my simulations.

Anyone can help?

Thank you very much in advance for your help.

Eva

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