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come4c

铁虫 (初入文坛)

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虫号: 1182015

[交流] 【求助】gromacs下对大分子体系QM/MM计算的问题

我用的是gromacs4.0.3+MOPAC7.0
模拟对象是MHC/VIRAL PEPTIDE/T-CELL RECEPTOR三者复合体(1AO7)，五条链，一共11000个原子，加上水和离子后270000左右的原子。
主要是计算MHC和VIRAL PEPTIDE的结合能，在这两者上分别取若干氨基酸用QM计算，其余用MM计算。整个体系能量最小化到1000一下，开始模拟是有如下错误，

      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

另外求教对大体系能量最小化应该怎么设置比较合理？emtol设到多少比较合适？constraints应该选用何种算法？

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1楼 2011-03-29 10:58:06

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sijifengsd

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★
come4c(金币+1):谢谢参与

呵呵，请问您用Gromacs设置qmmm连接原子的时候虚原子怎么写入gro文件的？这个问题我很感兴趣，但不知道怎么处理，谢谢赐教

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