[AMBER] Adding an atom to a residue by parmed

From: mish <smncbr.gmail.com>
Date: Fri, 1 Feb 2019 15:46:40 +0000

Dear all,

I am trying to modify amber parm7 files to generate parm7 files for
amino-acid side-chains in parmed. For this, I first created parm7 and top7
files of a complete amino-acid in leap (lets say, Trp). Then I deleted
backbone atoms (.N,H,CA,HA,C,O) and adjusted charge on CB using parmed:
parmed -p trp.parm7 -c trp.rst7
strip :1.N,H,CA,HA,C,O
change charge :1.CB -0.0346
outparm trp_sidechain.parm7 trp_sidechain.rst7

Everything seems to work well so far, but I still want to complete valency
of the CB carbon. Is there any straightforward way in parmed to add way to
add one more hydrogen (lest say HB1) to atom CB of residue :1 and copy all
the parameters from HB2 and HB3 in to HB1?

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Received on Fri Feb 01 2019 - 08:00:02 PST
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