hello everyone,
I want to construct the unit cell as the tutorial13 and do the
same work as the D.S.Cerutti's paper "Simulations of a protein crystal
with a high resolution X-ray structure: Evaluation of force fields and
water models." /J. Phys. Chem. B/ *114*:12811-12824.
As the paper, before MD simulation, we need to construct the
simulation Cell from 12 individual unit cells in a 2*2*3 arrangement and
then add ions and water. I do next using amber12:
1) ${AMBERHOME}/bin/PropPDB -p x1AHO.pdb -o x12_1AHO.pdb -X 45.9 -Y 40.7
-Z 30.1 -ix 2 -iy 2 -iz 3
2) ${AMBERHOME}/bin/AddToBox -c x12_1AHO.pdb -a Acetate.pdb -na 84 -o
xa1AHO.pdb -P 49727 -RP 4.0 -RW 6.0 -G 0.1 -V 1 -X 91.8 -Y 81.4 -Z 90.3
-al 90.0 -bt 90.0 -gm 90.0
3) ${AMBERHOME}/bin/AddToBox -c xa1AHO.pdb -a Ammonium.pdb -na 36 -o
xm1AHO.pdb -P 50315 -RP 4.0 -RW 6.0 -G 0.1 -V 1 -X 91.8 -Y 81.4 -Z 90.3
-al 90.0 -bt 90.0 -gm 90.0
4) ${AMBERHOME}/bin/AddToBox -c xm1AHO.pdb -a spce.pdb -na 9000 -o
solv1AHO.pdb -P 50315 -RP 4.0 -RW 6.0 -G 0.1 -V 1 -X 91.8 -Y 81.4 -Z
90.3 -al 90.0 -bt 90.0 -gm 90.0
5) tleap -s -f solvate.tLEaP
6) ${AMBERHOME}/bin/ChBox -c solv1AHO.crd -o solv1AHO.crd -X 91.8 -Y
81.4 -Z 90.3 -al 90.0 -bt 90.0 -gm 90.0
Question 1: I don't know whether these steps are right expecially
the (-X -Y -Z) value when proppdb ,addtobox and chbox------unit cell
box edge lengths (-X 45.9 -Y 40.7 -Z 30.1 )or supercell box edge
lengths (-X 91.8 -Y 81.4 -Z 90.3)?
Question2: I do "ambpdb -p solv1AHO.top <solv1AHO.crd
>solv1AHO1.pdb" and then use vmd to open solv1AHO1.pdb .But I see many
warning news such as "Warning) Unusual bond between residues: 3192
(none) and 1342 (waters) " and many water displaying gather together.Why?
After I finished the six step, I will do minimization using
solv1AHO.top and solv1AHO.crd .We do three minimization as the paper. In
the fist minimization,the final result energy is ****** .In the second
minimization, the min2.out result is also that and we got ************in
min2.rst. Then we can't do the third minimization .
Question3: why these energy are ***** and the bond energy is 0.000? Are
the top-file and crd-file I got wrong?
=====================
The tLEap file:
source leaprc.ff99SB
loadAmberPrep Acetate.prp
loadAmberPrep Ammonium.prp
ammparms = loadAmberParams Ammonium.frcmod
x = loadPdb "solv1AHO.pdb"
bond x.11.SG x.62.SG
bond x.15.SG x.35.SG
bond x.21.SG x.45.SG
bond x.25.SG x.47.SG
bond x.204.SG x.255.SG
bond x.208.SG x.228.SG
....................(there are many lines I can't display)
bond x.8710.SG x.8732.SG
bond x.8889.SG x.8940.SG
bond x.8893.SG x.8913.SG
bond x.8899.SG x.8923.SG
bond x.8903.SG x.8925.SG
bond x.9082.SG x.9133.SG
bond x.9086.SG x.9106.SG
bond x.9092.SG x.9116.SG
bond x.9096.SG x.9118.SG
setBox x vdw 1.0
saveAmberParm x solv1AHO.top solv1AHO.crd
quit
================================
The min1.in file :
initial minimisation restraint solvent particles ,added hydrogens
&cntrl
imin = 1,
maxcyc = 40000,
ncyc = 2000,
ntb = 1,
cut = 9.0
ntr = 1,restraintmask=':1-3072!.H=',
restraint_wt=1000.0,
/
and the min1.out file:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -3.4207E+09 1.5420E+06 8.3886E+06 O 87904
BOND = 188466.4833 ANGLE = 48742.9387 DIHED = 27311.6719
VDWAALS = ************* EEL = 2893801.6968 HBOND = 0.0000
1-4 VDW = 19497.2575 1-4 EEL = 141875.8611 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -2.8425E+08 1.5407E+06 8.3886E+06 O 71233
BOND = 188465.4924 ANGLE = 48742.9560 DIHED = 27311.6719
VDWAALS = ************* EEL = 2893818.9021 HBOND = 0.0000
1-4 VDW = 19497.2543 1-4 EEL = 141875.8649 RESTRAINT =
0.5613
EAMBER = *************
.............................................(there are many lines I
can't display)
NSTEP ENERGY RMS GMAX NAME NUMBER
2200 -8.4000E+09 2.8326E+05 8.3886E+06 O 32863
BOND = 0.0000 ANGLE = 138665.0194 DIHED = 28167.4538
VDWAALS = ************* EEL = 89742545.8658 HBOND = 0.0000
1-4 VDW = 85150.6573 1-4 EEL = 141892.0475 RESTRAINT =
0.0000
EAMBER = *************
.... RESTARTED DUE TO LINMIN FAILURE ...
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
2221 -8.3999E+09 2.8326E+05 8.3886E+06 O 32863
BOND = 0.0000 ANGLE = 138665.0203 DIHED = 28167.4538
VDWAALS = ************* EEL = 89742545.4937 HBOND = 0.0000
1-4 VDW = 85150.5481 1-4 EEL = 141892.0475 RESTRAINT =
0.0000
EAMBER = *************
***** REPEATED LINMIN FAILURE *****
===========================
The min2.in file:
initial minimisation restraint solvent particle
&cntrl
imin = 1,
maxcyc = 40000,
ncyc = 2000,
ntb = 1,
cut = 9.0
ntr = 1,restraintmask=':3073-18384',
restraint_wt=1000.0,
/
AND the min2.out file:
NSTEP ENERGY RMS GMAX NAME NUMBER
2050 -1.0153E+10 8.0112E+05 8.3886E+06 HB3 39147
BOND = 0.0000 ANGLE = 4108575.1870 DIHED = 116768.8191
VDWAALS = ************* EEL = -154872.1287 HBOND = 0.0000
1-4 VDW = ************* 1-4 EEL = 68200.0632 RESTRAINT =
0.0000
EAMBER = *************
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
2085 -1.0154E+10 8.0112E+05 8.3886E+06 HB3 39147
BOND = 0.0000 ANGLE = 4108575.1969 DIHED = 116768.8190
VDWAALS = ************* EEL = -154872.1019 HBOND = 0.0000
1-4 VDW = ************* 1-4 EEL = 68200.0630 RESTRAINT =
0.0000
EAMBER = *************
***** REPEATED LINMIN FAILURE *****
==========================
The vmd warning when loading solv1AHO1.pdb :
Warning) Unusual bond between residues: 3183 (none) and 2330 (waters)
Warning) Unusual bond between residues: 3183 (none) and 3109 (waters)
Warning) Unusual bond between residues: 3183 (none) and 5109 (waters)
Warning) Unusual bond between residues: 3183 (none) and 9587 (waters)
Warning) Unusual bond between residues: 3183 (none) and 2048 (waters)
Warning) Unusual bond between residues: 3183 (none) and 2078 (waters)
Warning) Unusual bond between residues: 3183 (none) and 2721 (waters)
Warning) Unusual bond between residues: 3183 (none) and 9587 (waters)
Warning) Unusual bond between residues: 3183 (none) and 213 (waters)
Warning) Unusual bond between residues: 3183 (none) and 982 (waters)
Warning) Unusual bond between residues: 3183 (none) and 1310 (waters)
Warning) Unusual bond between residues: 3183 (none) and 2048 (waters)
Warning) Unusual bond between residues: 3183 (none) and 2078 (waters)
Warning) Unusual bond between residues: 3183 (none) and 2721 (waters)
Warning) Unusual bond between residues: 3183 (none) and 3085 (waters)
Warning) Unusual bond between residues: 3183 (none) and 3364 (waters)
Warning) Unusual bond between residues: 3183 (none) and 5154 (waters)
Warning) Unusual bond between residues: 3183 (none) and 5562 (waters)
Warning) Unusual bond between residues: 3184 (none) and 9548 (waters)
Warning) Unusual bond between residues: 3184 (none) and 9548 (waters)
================
Thank you very much!
Yongxiu Li
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Received on Mon Apr 22 2013 - 05:30:03 PDT
