| 查看: 1638 | 回复: 1 | |||
[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？ |
回复此楼» 猜你喜欢
青B发送上会通知了吗
已经有14人回复
-
博士申请
已经有5人回复
-
4,4二甲基联苯干啥用，有懂得吗
已经有4人回复
-
某211大学教师把个人教师官方主页改成:我跑了我跑了我跑了!官宣跑路！
已经有6人回复
-
西安交大新媒学院副院长用撤稿论文结题
已经有7人回复
-
论文撤稿了
已经有9人回复
-
化学专业申博
已经有5人回复
-
招收2026级博士生
已经有5人回复
-
宿州学院学报
已经有3人回复
-
医学类期刊求推荐
已经有6人回复
» 本主题相关商家推荐: (我也要在这里推广)
» 本主题相关价值贴推荐，对您同样有帮助:
- 氨基酸在线衍生测定过程中遇到的一些问题
已经有6人回复
- 本人查阅文献，遇到一个问题，请教哪位给我解答哈，在下将不胜感激！
已经有18人回复
- 陕西省榆林市大能源体系建设2008-2018年重大项目规划表
已经有34人回复
- 面试时应对跳槽原因问题的诀窍
已经有7人回复
- 关于熵变的计算，有人知道怎么计算大的体系的熵变吗？比如将近一千个残基的体系？
已经有11人回复
- 分子模拟时间越长越好吗？
已经有44人回复
- AMBER中qm/mm的问题
已经有5人回复
- 求助各位，关于初学分子模拟
已经有9人回复
- 【求助】gromacs的又一个问题
已经有22人回复
- 【求助】psf文件的生成
已经有19人回复
» 抢金币啦！回帖就可以得到:
-
西安电子科技大学保研: 挑战高速IP设计NVMe，RDMA及NVMe-oF
+1/288
-
征结婚对象，男找女，坐标【北京】【北京】【北京】
+5/155
-
【专业EPR】：自由基(超氧、羟基、单线态氧)，空位缺陷；定量计算，VX: 761711562。
+1/91
-
诚邀津门师者共研
+1/76
-
真诚寻找另一半 觉得合适可以相互了解
+1/67
-
【通知】北京信息科技大学仪器科学与光电工程学院招收博士研究生（2026）
+2/50
-
【博士招生】江西理工大学招收博士研究生
+1/32
-
安徽农业大学招聘师资博士后以及人才引进教师
+1/24
-
【26.9月入学】211大学补招学博1人
+1/20
-
固体核磁测试求助
+1/10
-
南京农业大学2026年申请考核制博士招生：最后一批啦！
+1/9
-
电子科技大学材料学院SFT创新中心招收准备考研和读博的科研助理 理工医交叉方向
+1/9
-
能源电催化领域博士后招聘（高薪40万+）
+1/7
-
紧急招收2026年秋季入学博士生1名（河北工大/北京科技大学联合 增材制造/生物材料）
+1/5
-
地大武汉（211）招生光刻胶半导体方向博士生
+1/4
-
求助专利一篇，谢谢
+1/3
-
紧急招收2026年秋季入学博士生1名（河北工大/北京科技大学联合 增材制造/生物材料）
+1/3
-
【有偿访谈招募】高才通来港后，你过得还好吗？
+1/1
-
【有偿访谈招募】高才通来港后，你过得还好吗？
+1/1
-
一文看懂DNA损伤检测：守护生命蓝图的“基因体检”
+1/1
2楼2011-06-07 21:46:58