Dear all
I am calculating the relative binding energy of protein-dna and
protein-dna" complex using TI. I am
following the tutorial A9.
In second step, in minimization phase, job is stopped.
>>> output file:
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 6681
| Atom division among processors:
| 0 21890
Softcore Mask .1275,1276,1277,1280,1558,1559,1560,1561,1563,1565;
matches 10 atoms
this run corresponds to V1, its softcore atoms interact fully for
lambda=1
this process: 21890 atoms, partner process: 23383 atoms
SANDER BOMB in subroutine setup_sc
All non-softcore atoms must be identical in both systems
>>> input files:
min_v0_0.1
&cntrl
imin = 1, ntx = 1,
maxcyc = 2000, ntmin = 2,
ntpr = 100,
ntf = 1, ntc = 2,
ntb = 1, cut = 10.0,
icfe = 1, clambda = 0.1,
ifsc = 1,
crgmask = '.1275,1277,1279,1280,1281,1559,1561,1562,1563'
scmask = '.1275,1277,1279,1280,1281,1559,1561,1562,1563'
/
min_v1_0.1
&cntrl
imin = 1, ntx = 1,
maxcyc = 2000, ntmin = 2,
ntpr = 100,
ntf = 1, ntc = 2,
ntb = 1, cut = 10.0,
icfe = 1, clambda = 0.1,
ifsc = 1,
crgmask = '.1275,1276,1277,1280,1558,1559,1560,1561,1563,1565'
scmask = '.1275,1276,1277,1280,1558,1559,1560,1561,1563,1565'
/
Since number of Na ions for neutrality of the both systems is the same,
this difference in number of atoms corresponds to water molecules.
For this minimization, how to obtain inpcrd and prmtop files is as follows:
----------------------------------------------------------------
1)$AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03
2)complex_0 = loadpdb "complex_0.pdb"
3)addions complex_0 Na+ 0
4)solvatebox complex_0 TIP3PBOX 8.0 iso
*7179 water molecules were added.
*
5)eamberparm complex_0 complex_0.prmtop complex_0.inpcrd
----------------------------------------------------------------
1)$AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03
2)complex_1 = loadpdb "complex_1.pdb"
3)addions complex_1 Na+ 0
4)solvatebox complex_1 TIP3PBOX 8.0 iso
*6681 water molecules were added.*
5)eamberparm complex_1 complex_1.prmtop complex_1.inpcrd
----------------------------------------------------------------
Is there any way to add exact same number of water molecule to both systems?
Thanks in Advance.
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Received on Sun Feb 19 2012 - 04:00:02 PST
