AMBER Archive (2007)

Subject: AMBER: Getting prmtop and inpcrd

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Mon Oct 29 2007 - 09:43:44 CST

I had a lot of problems in fixing a large protein model. The last step was
using leal (leaprc.ff99SB in Amber9). Heavy atoms were added where I had set
TER records, res 111, 222, 333, and at res 444, besides 38 H/lone pairs. Both
prmtop and inpcrd could be saved (and opened correctly with VMD or Chimera).
The total charge is 24.000000. Not neutralized, not solvated, not tried to
minimize yet.

The last part of leap.log reads:

(Residues lacking connect 0/ connect 1 -
These don't have chain types marked:
res total affected
CTHR 4
NSER 4

Is that of concern or can I go on with these prmtop inpcrd?

Thanks
francesco pietra

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