[AMBER] TIP4PD water box error

From: Alexander Izvorski <aizvorski.gmail.com>
Date: Sun, 26 Dec 2021 14:47:53 -0800

Hello Amber folks - I tried using a TIP4PD water box instead of the more
usual TIP3P, and I just can't get it to work.

A minimal example in tleap looks like this:

source leaprc.protein.ff14SB
source leaprc.water.tip4pd
test = loadPdb 1fsc_amb.pdb
solvateBox test TIP4PDBOX 10.0
addIonsRand test CL 0
saveAmberParm test test.top test.crd

This definitely creates a water box, but saveAmberParm fails

Added 2629 residues.
Error: For atom (.R<WAT 62>.A<H1 2>) could not find vdW (or other)
parameters for type (HW)

(plus a few thousand identical errors)

The same works with leaprc.water.tip3p and TIP3PBOX (OPC also works). The
input file is from the tutorial (link
<https://ambermd.org/tutorials/pengfei/1fsc_amb.pdb>) not sure it matters
since I get the same errors with any pdb. My software version is
ambertools=21.11 from conda-forge on Ubuntu 20.04.

Mainly I wanted to use TIP4PD since that is the default for DE Shaw RNA
parameters (see my other post for an unrelated issue with that). I haven't
experimented that much with different kinds of water boxes so I'm not sure
what to do here. Any "tips" would be much appreciated!

Thanks and happy holidays!
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Received on Sun Dec 26 2021 - 15:00:03 PST
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