1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
|
#!/bin/bash
. ../MasterTest.sh
CleanFiles xtals.in mdAsuOnly.pdb mdSolventByAtom.pdb mdSolventByMolecule.pdb
TESTNAME='XtalSymm tests'
Requires netcdf notparallel
INPUT="-i xtals.in"
# Simple reimaging of just the asymmetric unit
cat > xtals.in << EOF
parm ../x6dky.parm7
trajin ../mdXtal.nc
reference ../mdXtal.inpcrd
xtalsymm :1-16 reference group P22(1)2(1) na 2 nb 1 nc 1
trajout mdAsuOnly.pdb chainid ' '
EOF
RunCpptraj "XtalSymm Reference"
DoTest mdAsuOnly.pdb.save mdAsuOnly.pdb
# Reimaging of the entire solvent, atom by atom
cat > xtals.in << EOF
parm ../x6dky.parm7
trajin ../mdXtal.nc
reference ../mdXtal.inpcrd
xtalsymm :1-16 reference group P22(1)2(1) na 2 nb 1 nc 1 collect
trajout mdSolventByAtom.pdb chainid ' '
EOF
RunCpptraj "XtalSymm Reimaging by Atom"
DoTest mdSolventByAtom.pdb.save mdSolventByAtom.pdb
# Reimaging of the entire solvent, atom by atom
cat > xtals.in << EOF
parm ../x6dky.parm7
trajin ../mdXtal.nc
reference ../mdXtal.inpcrd
xtalsymm :1-16 reference group P22(1)2(1) na 2 nb 1 nc 1 collect centroid
trajout mdSolventByMolecule.pdb chainid ' '
EOF
RunCpptraj "XtalSymm Reimaging by Molecule"
DoTest mdSolventByMolecule.pdb.save mdSolventByMolecule.pdb
EndTest
exit 0
|
