Hello, just reawakening this thread because I find that I have difficulties
setting up SPCFW also.
My leap input looks like this:
source leaprc.ff99brc0
##SPCFW commands:
loadAmberParams frcmod.spcfw
set default FlexibleWater on
nuc = loadpdb gc12mer_Z.pdb
addions nuc Na+ 22
solvatebox nuc SPCBOX 20
saveamberparm nuc gc12_Z.top gc12_Z.crd
and my leap output looks all fine apart from some warnings at the end:
.
.
.
Loading library: /usr/local/amber11//dat/leap/lib/solvents.lib
.
.
.
Checking Unit.
WARNING: There is a bond of 3.297303 angstroms between:
------- .R<DG3 12>.A<O3' 33> and .R<DG3 12>.A<H3T 34>
WARNING: There is a bond of 3.297842 angstroms between:
------- .R<DG3 24>.A<O3' 33> and .R<DG3 24>.A<H3T 34>
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
1-4: angle 778 779 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 1393 1394 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 1396 1397 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 1399 1400 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 1402 1403 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 1405 1406 duplicates bond ('triangular' bond) or angle ('square'
bond)
.
.
.
etc etc etc one warning per water molecule. Does this mean that I have
somehow picked up both triangular-bond (rigid model) and angle (flexible
model) terms?
Before anyone tells me that I should have used "SPCFBOX" instead of "SPCBOX"
(as suggested in the amberTools v1.4 manual, 2.10 "Solvent Models")... this
just gets an error message from leap, even though "solvents.lib" is loaded;
eg:
>solvatebox nuc SPCFBOX 25
solvateBox: Argument #1 is type String must be of type: [unit]
usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
I is the confusingeds about this, I'm not even sure I need flexible water
anymore but surely there has to be a way....
Josh
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Received on Tue Jan 25 2011 - 07:00:02 PST
