标题: 经过phbuilder编译之后的gmx跑出来的结果，基于VMD分析盐桥时应如何处理氨基酸 [打印本页] 作者Author: 停云云 时间: 2026-1-14 11:09 标题: 经过phbuilder编译之后的gmx跑出来的结果，基于VMD分析盐桥时应如何处理氨基酸 各位老师好！
我尝试基于phbuilder（https://pypi.org/project/phbuilder/）编译后的gmx来分析在不同pH环境下蛋白质。我在分析盐桥这个参数的时候遇到问题，我之前用正常版本的gmx已经分析过盐桥，按照卢老师培训课程，在vmd中操作，操作大概步骤如https://blog.csdn.net/xiaolan39/article/details/121939901所示。但这次在分析时候，遇到报错如下：
No oxygens of acidic amino acid residues were found in the given selection.No nitrogens of basic amino acid residues were found in the given selection.No oxygens of acidic amino acid residues were found in the given selection.No nitrogens of basic amino acid residues were found in the given selection. while executing"error $errMsg" (procedure "findSaltBridges" line 30) invoked from within"findSaltBridges $sel $updateSel $COMDist $ONDist $frames_begin $frames_step $frames_end pairs idpairs" (procedure "::saltbr::saltbr" line 215) invoked from within"::saltbr::saltbr -gui 1 -ondist $::saltbr::guiONDist -comdist $::saltbr::guiCOMDist -writefiles $::saltbr::guiWriteAll -outdir $::saltbr::guiOutdir -f..." invoked from within".saltbr.control.button invoke" ("uplevel" body line 1) invoked from within"uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 22) invoked from within"tk::ButtonUp .saltbr.control.button" (command bound to event)
我去vmd找了其对于盐桥的定义为：
Acidic and basic residuesThe Salt Bridges plugin searches for salt bridges between amino acid residues identified with the VMD keywords acidic and basic, which are defined in the following way:atomselect macro acidic "resname ASP GLU"atomselect macro basic "resname ARG HIS LYS HSP"
但是在我的最终pdb结果中（可以理解为跑完md后那个gro文件），其对以上氨基酸定位都在氨基酸最后加了一个T，如LYS变为LYST，我明白这是在处理蛋白质在酸性或者碱性条件下进行的一种处理。我也尝试了gmx saltbr这个用法，当然一如既往的难用。
发帖目的是想询问大家，在这种情况下如何进行盐桥分析，如果有有经验的老师麻烦赐教一二！感激！