通过antechamber方法构建拓扑文件后计算出错

02130213aaa

我通过antechamber+acpype方法得到分子的拓扑文件，然后在GAFF力场中补充了原子类型，但是进行体系能量最小化的时候出现了这样的错误提示。第一，体系电荷不是零。我构建的体系是水+水杨酸+磷酸三丁酯。是否因为水杨酸在水中轻微电离导致电荷变化呢，该如何更改？
第二，原子名称不匹配。这个不知道如何改啊。
请各位老师帮帮我！谢谢！！！！

NOTE 1 [file mix.top, line 16]:
  System has non-zero total charge: 0.000193
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.
  




Warning: atom name 1 in mix.top and mix.pdb does not match (OW - H)
Warning: atom name 2 in mix.top and mix.pdb does not match (HW1 - H)
Warning: atom name 3 in mix.top and mix.pdb does not match (HW2 - O)
Warning: atom name 4 in mix.top and mix.pdb does not match (OW - H)
Warning: atom name 5 in mix.top and mix.pdb does not match (HW1 - H)
Warning: atom name 6 in mix.top and mix.pdb does not match (HW2 - O)
Warning: atom name 7 in mix.top and mix.pdb does not match (OW - H)
Warning: atom name 8 in mix.top and mix.pdb does not match (HW1 - H)
Warning: atom name 9 in mix.top and mix.pdb does not match (HW2 - O)
Warning: atom name 10 in mix.top and mix.pdb does not match (OW - H)
Warning: atom name 11 in mix.top and mix.pdb does not match (HW1 - H)
Warning: atom name 12 in mix.top and mix.pdb does not match (HW2 - O)
Warning: atom name 13 in mix.top and mix.pdb does not match (OW - H)
Warning: atom name 14 in mix.top and mix.pdb does not match (HW1 - H)
Warning: atom name 15 in mix.top and mix.pdb does not match (HW2 - O)
Warning: atom name 16 in mix.top and mix.pdb does not match (OW - H)
Warning: atom name 17 in mix.top and mix.pdb does not match (HW1 - H)
Warning: atom name 18 in mix.top and mix.pdb does not match (HW2 - O)
Warning: atom name 19 in mix.top and mix.pdb does not match (OW - H)
Warning: atom name 20 in mix.top and mix.pdb does not match (HW1 - H)
(more than 20 non-matching atom names)


WARNING 1 [file mix.top, line 16]:
  16705 non-matching atom names
  atom names from mix.top will be used
  atom names from mix.pdb will be ignored




Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:  2651      Water residues
There are:   218      Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 50112.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 96x96x96, spacing 0.105 0.105 0.105
Estimate for the relative computational load of the PME mesh part: 0.73


NOTE 2 [file em.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing.




This run will generate roughly 98 Mb of data


There were 2 notes


There was 1 warning

五月雨

wx91aaa 发表于 2017-7-27 18:14
感谢sob老师的指导，MD已经顺利跑完了。我是做溶剂萃取动力学模拟的，看文献中用到的力场是用OPLS/AA ...

请问楼主是如何在GROMACS里使用GAFF力场的，我在GROMACS目录里面没有找到关于GAFF力场的文件
已经解决

wx91aaa

sobereva 发表于 2017-7-27 18:22
GAFF完全没问题

好的！谢谢老师！！！

sobereva

wx91aaa 发表于 2017-7-27 18:14
感谢sob老师的指导，MD已经顺利跑完了。我是做溶剂萃取动力学模拟的，看文献中用到的力场是用OPLS/AA ...

GAFF完全没问题

wx91aaa

sobereva 发表于 2017-7-27 08:59
意义不明。itp文件哪来的？是指水的itp么？水的itp在每个力场目录下都有，用哪个力场时就应该用哪个力 ...

感谢sob老师的指导，MD已经顺利跑完了。我是做溶剂萃取动力学模拟的，看文献中用到的力场是用OPLS/AA，但是我做的是用GAFF力场，这样可以吗？再次谢谢老师！

sobereva

02130213aaa 发表于 2017-7-26 20:51
谢谢sob老师！我的top文件力场是用的amber的，itp文件应该是原来gromacs里面的。这样的话是该引入gromacs ...

意义不明。itp文件哪来的？是指水的itp么？水的itp在每个力场目录下都有，用哪个力场时就应该用哪个力场目录下的水的itp。如果当前用GAFF力场，水的itp就用amber力场目录下的

02130213aaa

sobereva 发表于 2017-7-26 02:08
1 这样稍微偏离0没关系。有可能是itp里的原子电荷加和不精确为零，也可能是浮点数的记录精度问题，提示中的 ...

谢谢sob老师！我的top文件力场是用的amber的，itp文件应该是原来gromacs里面的。这样的话是该引入gromacs的力场呢？还是在做一下水的拓扑文件补充在GAFF力场里面呢？

sobereva

1 这样稍微偏离0没关系。有可能是itp里的原子电荷加和不精确为零，也可能是浮点数的记录精度问题，提示中的那个链接里有讨论。这根电离毫无关系。

2 这是因为top里引入的水分子itp文件里的原子顺序和pdb文件里不同造成的。比如可能水的itp里是O,H,H顺序，但是pdb里是H,H,O顺序。顺序匹配不上没法进行模拟（但原子名不匹配倒没关系）。