老师好，大家好，请问怎样在GAFF下跑隐式溶剂模型？我提交任务后得到：
GB parameter(s) missing or negative for atom type 'cc'
GB parameter(s) missing or negative for atom type 'na'
GB parameter(s) missing or negative for atom type 'hn'
GB parameter(s) missing or negative for atom type 'h4'
GB parameter(s) missing or negative for atom type 'ha'
GB parameter(s) missing or negative for atom type 's'
GB parameter(s) missing or negative for atom type 'Li'
Fatal error:
Can't do GB electrostatics; the implicit_genborn_params section of the
forcefield is missing parameters for 7 atomtypes or they might be negative.
作者Author: yihanxu 时间: 2019-4-6 05:51
如果用的是默认的ACE approximation方法计算非极性部分，所涉及的溶剂探针半径是在哪里设置的呢？谢谢。作者Author: sobereva 时间: 2019-4-6 05:58
gmx在GAFF下没法直接跑GB模型，你得提供类似自带的amber目录下的gbsa.itp文件那样的GB参数才行。有些GAFF的原子类型实质上和AMBER是等同的，这些可以挪过去用作者Author: 黑色幽默pxj 时间: 2020-7-22 05:49
请问楼主最后这个问题怎么解决的呢？我也遇到相似的问题，不过我用的charmm力场，我的蛋白里面有金属原子，再用隐式溶剂跑的时候也遇到相同错误
GB parameter(s) missing or negative for atom type 'MG'
GB parameter(s) missing or negative for atom type 'CAL'
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Program gmx grompp, VERSION 5.1.2
Source code file: /export/src/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c, line: 1303
Fatal error:
Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 2 atomtypes or they might be negative.
For more information and tips for troubleshooting, please check the GROMACS