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【求助】gromacs下对大分子体系QM/MM计算的问题
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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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2楼2011-06-07 21:46:58