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标题: GROMACS能否模拟既有DNA又有RNA的杂链？ [打印本页]

作者
Author: 17-li 时间: 2025-5-22 09:34
标题: GROMACS能否模拟既有DNA又有RNA的杂链？
我有一个核酸体系，由3条纯RNA链和3条RNA1-DNA1-RNA2-DNA2杂交链通过碱基互补配对形成四面体结构（见下面的图）。在第一步结构转换就出现了报错：
命令为，所用力场为 amber14sb_OL15.ff：

gmxpdb2gmx -f BIRDS_forGMX.pdb-o birds.gro -p topol.top -water tip3p-ter -ignh

报错为：

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Program: gmx pdb2gmx, version 2022.4

Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp(line 1040)

Fatal error:

The residues in the chainA1--DG63 do not have a consistent type. The first

residue has type 'RNA',while residue DA9 is of type 'DNA'. Either there is a

mistake in your chain, or it includes nonstandardresidue names that have not

yet been added to the residuetypes.dat file in theGROMACS library directory.

If there are other molecules such as ligands, theyshould not have the same

chain ID as the adjacent protein chain since it's aseparate molecule.

For more information and tips for troubleshooting,please check the GROMACS

website athttp://www.gromacs.org/Documentation/Errors

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请问各位老师，GROMACS要求同一链内的所有残基类型必须一致吗？如果是这样，有什么别的办法可以模拟我的杂交链体系吗？

作者
Author: sobereva 时间: 2025-5-22 09:57
手动把结构文件里DNA和RNA部分设成不同的链名就完了

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