x2top创建碳纳米管失败

wanzongliang

我在MS里创建了一个碳纳米管，后想用gromacs创建top文件，但创建的过程出现了问题，经过我反复的测试我发现是周期性的问题，想请教一下各位老师，有没有人有关于这方面的经验，我创建的碳纳米管文件附上，我用vmd查看其周期性是正确的，如图，最后x2top的时候出现的报错是

$ gmx-2023.3 x2top -f SWNT_try1.gro -o SWNT.top -ff select -noparam -pbc
                      :-) GROMACS - gmx x2top, 2023.3 (-:


Executable:   gmx-2023.exe
Data prefix:  /home/wzl/gromacs-2023.3/opt/gromacs/2023.3
Working dir:  /home/wzl/md/nano
Command line:
  gmx-2023.3 x2top -f SWNT_try1.gro -o SWNT.top -ff select -noparam -pbc


Select the Force Field:


From current directory:


1: Graphene and C3N4 force field based on OPLS-AA/L all-atom force field


From '/home/wzl/gromacs-2023.3/opt/gromacs/2023.3/share/gromacs/top':


2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)


3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)


4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)


5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)


6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)


7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)


8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)


9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)


10: GROMOS96 43a1 force field


11: GROMOS96 43a2 force field (improved alkane dihedrals)


12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)


13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)


14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)


15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)


16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
1
Opening force field file ./gra_cn.ff/atomname2type.n2t


There are 5 name to type translations in file ./gra_cn.ff


Generating bonds from distances...
Can not find forcefield for atom C1-9 with 5 bonds
Can not find forcefield for atom C4-12 with 5 bonds
Can not find forcefield for atom C8-16 with 5 bonds
Can not find forcefield for atom C12-20 with 5 bonds
Can not find forcefield for atom C16-24 with 5 bonds
Can not find forcefield for atom C20-28 with 5 bonds
Can not find forcefield for atom C24-32 with 5 bonds
Can not find forcefield for atom C28-36 with 5 bonds
Can not find forcefield for atom C32-40 with 5 bonds
Can not find forcefield for atom C36-44 with 5 bonds
Can not find forcefield for atom C40-48 with 5 bonds
Can not find forcefield for atom C44-52 with 5 bonds
Can not find forcefield for atom C48-56 with 5 bonds
Can not find forcefield for atom C52-60 with 5 bonds
Can not find forcefield for atom C56-64 with 5 bonds
Can not find forcefield for atom C60-68 with 5 bonds
Can not find forcefield for atom C64-72 with 5 bonds
Can not find forcefield for atom C68-76 with 5 bonds
Can not find forcefield for atom C72-80 with 5 bonds
Can not find forcefield for atom C53-543 with 4 bonds
Can not find forcefield for atom C53-546 with 4 bonds
Can not find forcefield for atom C54-550 with 4 bonds
Can not find forcefield for atom C54-554 with 4 bonds
Can not find forcefield for atom C55-558 with 4 bonds
Can not find forcefield for atom C55-562 with 4 bonds
Can not find forcefield for atom C55-566 with 4 bonds
Can not find forcefield for atom C56-570 with 4 bonds
Can not find forcefield for atom C56-574 with 4 bonds
Can not find forcefield for atom C57-578 with 4 bonds
Can not find forcefield for atom C57-582 with 4 bonds
Can not find forcefield for atom C57-586 with 4 bonds
Can not find forcefield for atom C58-590 with 4 bonds
Can not find forcefield for atom C58-594 with 4 bonds
Can not find forcefield for atom C59-598 with 4 bonds
Can not find forcefield for atom C59-602 with 4 bonds
Can not find forcefield for atom C59-606 with 4 bonds
Can not find forcefield for atom C60-610 with 4 bonds
Can not find forcefield for atom C60-614 with 4 bonds


-------------------------------------------------------
Program:     gmx x2top, version 2023.3
Source file: src/gromacs/gmxpreprocess/x2top.cpp (line 179)


Fatal error:
Could only find a forcefield type for 602 out of 640 atoms


For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
附上我的n2t文件，请教一下有没有老师知道我这是哪里出现的问题

wanzongliang

sobereva 发表于 2024-3-12 19:57
我刚才又仔细看了下，是盒子边界原子和镜像原子重合了。需要删除多余的。例如画红圈的两个原子实际上是重 ...

哦哦哦感谢sob老师我明白了

sobereva

wanzongliang 发表于 2024-3-12 19:57
哦哦哦感谢sob老师

我刚才又仔细看了下，是盒子边界原子和镜像原子重合了。需要删除多余的。例如画红圈的两个原子实际上是重合的

wanzongliang

sobereva 发表于 2024-3-12 19:53
跟周期性没关系。当前gro里的盒子信息没问题，在VMD中显示周期镜像，可以看到在盒子边界地方没有异常
纯粹 ...

哦哦哦感谢sob老师

sobereva

跟周期性没关系。当前gro里的盒子信息没问题，在VMD中显示周期镜像，可以看到在盒子边界地方没有异常
纯粹是n2t文件写的问题
自从我开发了更好用的sobtop后我就再也不用x2top。http://sobereva.com/soft/Sobtop里面有用于周期性的例子，assign_AT.dat文件的设置比n2t灵活得多