Protonated aspartic acid

From: apw397_at_soton.ac.uk
Date: Wed Mar 24 2004 - 06:10:11 CST

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I am trying to use a protonated aspartic acid (CHARM27 forcefield ) and when running through
psfgen I use residue name ASPP for the non-backbone atoms. psfgen seems
to recognise the residue patch (ie ASPP being part of the ASP residue) however removes the
vital proton neutralising the residue.

I have got around this be creating a new residue that includes the ASP
backbons and the ASPP patch atoms in the CHARM topology file. I am
unsure about the way I have manually combined these however and would
prefer not to use this!

Anyone else used protonated acid patches?

Advice welcome!

Adrian Wiley

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