使用packmol建盒子原子与拓扑文件不对应

二饼妹

使用acpype生成的GAFF力场拓扑，氯化胆碱+乙酰丙酸，盒子大小为6*6*6，有两个问题：
1，用gmx insert-molecules分别加Ch+,Cl-,乙酰丙酸150，150，300，最多能加200：400的，但是我用packmol都可以加500：1000的，这是为什么呢？
2，我是用packmol放了150：300的粒子，但是开始跑的时候出现如下报错，应该是itp里和pdb里原子名不对应，我想使用packmol建盒子，这应该怎么办呢？
gmx grompp -f em.mdp -c 150.pdb -p chlev.top -o em.tpr


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Setting the LD random seed to 110299978
Generated 91 of the 91 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 91 of the 91 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'ch'
Excluding 1 bonded neighbours molecule type 'CL'
Excluding 3 bonded neighbours molecule type 'lev'
Warning: atom name 1 in chlev.top and 150.pdb does not match (C1 - C)
Warning: atom name 2 in chlev.top and 150.pdb does not match (H2 - H)
Warning: atom name 3 in chlev.top and 150.pdb does not match (H3 - H)
Warning: atom name 4 in chlev.top and 150.pdb does not match (H4 - H)
Warning: atom name 5 in chlev.top and 150.pdb does not match (C5 - C)
Warning: atom name 6 in chlev.top and 150.pdb does not match (H6 - H)
Warning: atom name 7 in chlev.top and 150.pdb does not match (H7 - H)
Warning: atom name 8 in chlev.top and 150.pdb does not match (H8 - H)
Warning: atom name 9 in chlev.top and 150.pdb does not match (C9 - C)
Warning: atom name 10 in chlev.top and 150.pdb does not match (H10 - H)
Warning: atom name 11 in chlev.top and 150.pdb does not match (H11 - H)
Warning: atom name 12 in chlev.top and 150.pdb does not match (H12 - H)
Warning: atom name 13 in chlev.top and 150.pdb does not match (C13 - C)
Warning: atom name 14 in chlev.top and 150.pdb does not match (H14 - H)
Warning: atom name 15 in chlev.top and 150.pdb does not match (H15 - H)
Warning: atom name 16 in chlev.top and 150.pdb does not match (C16 - C)
Warning: atom name 17 in chlev.top and 150.pdb does not match (H17 - H)
Warning: atom name 18 in chlev.top and 150.pdb does not match (H18 - H)
Warning: atom name 19 in chlev.top and 150.pdb does not match (N19 - N)
Warning: atom name 20 in chlev.top and 150.pdb does not match (O20 - O)
(more than 20 non-matching atom names)

WARNING 1 [file chlev.top, line 24]:
  7950 non-matching atom names
  atom names from chlev.top will be used
  atom names from 150.pdb will be ignored


Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:   450      Other residues
There are:   150        Ion residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 24297.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 52x52x52, spacing 0.116 0.116 0.116
Estimate for the relative computational load of the PME mesh part: 0.22
This run will generate roughly 48 Mb of data

There was 1 warning

-------------------------------------------------------
Program:     gmx grompp, version 2016.4
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2325)

Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


附件分别是氯化胆碱阳离子部分和乙酰丙酸的itp和pdb文件

牧生

gmx insert-molecules加入氯离子，远不如gmx genion -s XXXXX.tpr -o XXXXX.gro -neutral -p XXXX.top   这个命令好。直接使体系为电中性。

只是名字对不上，我觉得是可以忽视这些的   命令后加上   -maxwarn 1

sobereva

insert-molecules的算法非常简单，没有packmol考虑那么周到。前者是一个一个加，直到插不进去为止，而后者在构建过程中会不断调节所有分子的位置和朝向，显然后者才有可能生成更致密的盒子。

结构文件和拓扑文件里的原子名不一致不用管，原子顺序对了就行。当前原子顺序是对应的。

二饼妹

sobereva 发表于 2021-2-1 20:05
insert-molecules的算法非常简单，没有packmol考虑那么周到。前者是一个一个加，直到插不进去为止，而后者 ...

谢谢老师，我把上面那个报错用-maxwarn 1忽略之后，我的能量最小化只能进行几十步，感觉没有收敛，这应该怎么办呢，是我画的分子有问题么？em.mdp如下：
define = -DFLEXIBLE
integrator = steep
nsteps = 10000
emtol  = 1.0
emstep = 0.01
;
nstxout   = 20
nstlog    = 50
nstenergy = 50
;
pbc = xyz
cutoff-scheme            = Verlet
coulombtype              = PME
rcoulomb                 = 1.5
vdwtype                  = cut-off
rvdw                     = 1.5
DispCorr                 = EnerPres
;
constraints              = none

sobereva

二饼妹 发表于 2021-2-1 20:30
谢谢老师，我把上面那个报错用-maxwarn 1忽略之后，我的能量最小化只能进行几十步，感觉没有收敛，这应该 ...

跟那个warning没任何直接关系

做em的目的是为了md能跑，先看md能不能跑再说