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come4c

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[交流] 【求助】gromacs下對大分子體系QM/MM計(jì)算的問題

我用的是gromacs4.0.3+MOPAC7.0
模擬對象是MHC/VIRAL PEPTIDE/T-CELL RECEPTOR三者復(fù)合體(1AO7)，五條鏈，一共11000個(gè)原子，加上水和離子后270000左右的原子。
主要是計(jì)算MHC和VIRAL PEPTIDE的結(jié)合能，在這兩者上分別取若干氨基酸用QM計(jì)算，其余用MM計(jì)算。整個(gè)體系能量最小化到1000一下，開始模擬是有如下錯(cuò)誤，

      RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 35
keywords are: PRECISE GEO-OK CHARGE=0 GRAD MMOK ANALYT AM1

Back Off! I just backed up qmmm.trr to ./#qmmm.trr.1#

Back Off! I just backed up qmmm.xtc to ./#qmmm.xtc.1#

Back Off! I just backed up qmmm.edr to ./#qmmm.edr.1#

WARNING: This run will generate roughly 3863 Mb of data

starting mdrun 'HLA-A 0201'
5000 steps,    5.0 ps.
counting the number of NH-C=O groups
step 0

Step 44, time 0.044 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000010, max 0.000487 (between atoms 2254 and 2257)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
3941 3942 34.1 0.0945 0.0945    0.0945

Step 45, time 0.045 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000013, max 0.000668 (between atoms 2254 and 2257)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
3941 3942 41.1 0.0945 0.0945    0.0945

Step 46, time 0.046 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000017, max 0.000853 (between atoms 2254 and 2256)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
3941 3942 49.3 0.0945 0.0945    0.0945

Step 47, time 0.047 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000023, max 0.001332 (between atoms 2254 and 2256)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
3941 3942 58.9 0.0945 0.0945    0.0945

ALL CONVERGERS ARE NOW FORCED ON
SHIFT=10, PULAY ON, CAMP-KING ON
AND ITERATION COUNTER RESET

MAXIMUM SIZE: 9
EMAT
0.100000E+01-0.100000E+01
-0.100000E+01 0.000000E+00
EMAT
Infinity    0.000000E+00
0.000000E+00 0.000000E+00

Step 48, time 0.048 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000034, max 0.001928 (between atoms 2254 and 2256)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
3941 3942 70.1 0.0945 0.0945    0.0945

Step 49, time 0.049 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000059, max 0.002527 (between atoms 3941 and 3942)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
3941 3942 90.0 0.0945 0.0947    0.0945
2254 2256 30.9 0.1012 0.1012    0.1010

t = 0.049 ps: Water molecule starting at atom 272720 can not be settled.
Check for bad contacts and/or reduce the timestep.

Back Off! I just backed up step49b.pdb to ./#step49b.pdb.1#

Back Off! I just backed up step49c.pdb to ./#step49c.pdb.1#
Wrote pdb files with previous and current coordinates

Step 50, time 0.05 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000399, max 0.028944 (between atoms 3941 and 3942)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
3941 3942 90.0 0.0947 0.0972    0.0945
2254 2256 34.1 0.1012 0.1012    0.1010

t = 0.050 ps: Water molecule starting at atom 272852 can not be settled.
Check for bad contacts and/or reduce the timestep.

Back Off! I just backed up step50b.pdb to ./#step50b.pdb.1#

Back Off! I just backed up step50c.pdb to ./#step50c.pdb.1#
Wrote pdb files with previous and current coordinates

Step 51, time 0.051 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000548, max 0.039885 (between atoms 3941 and 3942)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
3941 3942 90.0 0.0972 0.0983    0.0945
2254 2256 35.2 0.1012 0.1012    0.1010

t = 0.051 ps: Water molecule starting at atom 272720 can not be settled.
Check for bad contacts and/or reduce the timestep.

Back Off! I just backed up step51b.pdb to ./#step51b.pdb.1#

Back Off! I just backed up step51c.pdb to ./#step51c.pdb.1#
Wrote pdb files with previous and current coordinates

Step 52, time 0.052 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000232, max 0.016477 (between atoms 3941 and 3942)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
3941 3942 90.0 0.0983 0.0961    0.0945
2254 2256 33.8 0.1011 0.1010    0.1010

ALL CONVERGERS ARE NOW FORCED ON
SHIFT=10, PULAY ON, CAMP-KING ON
AND ITERATION COUNTER RESET

MAXIMUM SIZE: 2
EMAT
0.100000E+01-0.100000E+01
-0.100000E+01 0.000000E+00
EMAT
Infinity    0.000000E+00
0.000000E+00 0.000000E+00

Step 53, time 0.053 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000045, max 0.002539 (between atoms 2254 and 2257)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
3941 3942 84.1 0.0960 0.0945    0.0945
2254 2256 30.3 0.1010 0.1009    0.1010

t = 0.053 ps: Water molecule starting at atom 272720 can not be settled.
Check for bad contacts and/or reduce the timestep.

Back Off! I just backed up step53b.pdb to ./#step53b.pdb.1#

Back Off! I just backed up step53c.pdb to ./#step53c.pdb.1#
Wrote pdb files with previous and current coordinates

ALL CONVERGERS ARE NOW FORCED ON
SHIFT=10, PULAY ON, CAMP-KING ON
AND ITERATION COUNTER RESET

      """""""""""""UNABLE TO ACHIEVE SELF-CONSISTENCE

      DELTAE=  -0.1994E-03    DELTAP=  NaN

-------------------------------------------------------------------------------
PRECISE GEO-OK CHARGE=0 GRAD MMOK ANALYT AM1

   A FAILURE HAS OCCURRED, TREAT RESULTS WITH CAUTION!!
   ++++----**** FAILED TO ACHIEVE SCF. ****----++++

                              AM1 CALCULATION
                                                   VERSION  7.00
                                                   Sun Mar 27 22:07:56 2011

FOR SOME REASON THE SCF CALCULATION FAILED.
THE RESULTS WOULD BE MEANINGLESS, SO WILL NOT BE PRINTED.
TRY TO FIND THE REASON FOR THE FAILURE BY USING "PL".
CHECK YOUR GEOMETRY AND ALSO TRY USING SHIFT OR PULAY.

ATOM CHEMICAL  BOND LENGTH BOND ANGLE    TWIST ANGLE
NUMBER  SYMBOL (ANGSTROMS)    (DEGREES)    (DEGREES)
(I)                NA:I       NB:NA:I    NC:NB:NA:I    NA NB NC

   1    N
   2    H  0.00000                                  0
   3    C  0.00000       0.00000                   0 0
   4    H  0.00000       0.00000    0.00000    0 0 0
   5    C  0.00000       0.00000    0.00000    0 0 0
   6    H  0.00000       0.00000    0.00000    0 0 0
   7    H  0.00000       0.00000    0.00000    0 0 0
   8    H  0.00000       0.00000    0.00000    0 0 0
   9    C  0.00000       0.00000    0.00000    0 0 0
   10    O  0.00000       0.00000    0.00000    0 0 0
   11    H  0.00000       0.00000    0.00000    0 0 0
   12    H  0.00000       0.00000    0.00000    0 0 0
   13    N  0.00000       0.00000    0.00000    0 0 0
   14    C  0.00000       0.00000    0.00000    0 0 0
   15    H  0.00000       0.00000    0.00000    0 0 0
   16    C  0.00000       0.00000    0.00000    0 0 0
   17    H  0.00000       0.00000    0.00000    0 0 0
   18    H  0.00000       0.00000    0.00000    0 0 0
   19    C  0.00000       0.00000    0.00000    0 0 0
   20    H  0.00000       0.00000    0.00000    0 0 0
   21    H  0.00000       0.00000    0.00000    0 0 0
   22    C  0.00000       0.00000    0.00000    0 0 0
   23    H  0.00000       0.00000    0.00000    0 0 0
   24    H  0.00000       0.00000    0.00000    0 0 0
   25    C  0.00000       0.00000    0.00000    0 0 0
   26    O  0.00000       0.00000    0.00000    0 0 0
   27    H  0.00000       0.00000    0.00000    0 0 0
   28    H  0.00000       0.00000    0.00000    0 0 0

另外求教對大體系能量最小化應(yīng)該怎么設(shè)置比較合理？emtol設(shè)到多少比較合適？constraints應(yīng)該選用何種算法？

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come4c(金幣+1):謝謝參與

呵呵，請問您用Gromacs設(shè)置qmmm連接原子的時(shí)候虛原子怎么寫入gro文件的？這個(gè)問題我很感興趣，但不知道怎么處理，謝謝賜教

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