如何分析由于N/C端带电而产生的盐桥？

bingzan · 发表于 Post on 2023-5-20 23:29:39

老师好，

我的多肽N端是NH3+-GLY，C端是SER-COO-，想统计GLY与SER形成的盐桥。selection输入resname GLY SER，发现vmd会报错selection里找不到O/N原子。是不是因为vmd只能找酸性碱性氨基酸之间的盐桥？
请问应该怎么解决？谢谢！
报错信息如下：
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)

bingzan · 发表于 Post on 2023-5-21 20:00:00

sobereva 发表于 2023-5-21 16:21
估计没戏
定义应该是插件内部的

好的，我明白了。谢谢老师!

sobereva · 发表于 Post on 2023-5-21 16:21:21

bingzan 发表于 2023-5-21 09:00
我看到帮助里写：
atomselect macro acidic "resname ASP GLU"
atomselect macro basic "resname ARG H ...

估计没戏
定义应该是插件内部的

bingzan · 发表于 Post on 2023-5-21 09:00:48

sobereva 发表于 2023-5-21 03:55
帮助里有明确说明：http://www.ks.uiuc.edu/Research/vmd/plugins/saltbr/

其它的盐桥自己写脚本根据原 ...

我看到帮助里写：
atomselect macro acidic "resname ASP GLU"
atomselect macro basic "resname ARG HIS LYS HSP"

我想尝试重新定义，把SER和GLY分别添加到acidic和basic里面，在vmd命令行窗口写：
atomselect macro acidic "resname ASP GLU SER"
atomselect macro basic "resname ARG HIS LYS HSP GLY"

但是会出现同样的报错，请问这个方法是不是行不通？

sobereva · 发表于 Post on 2023-5-21 03:55:48

帮助里有明确说明：http://www.ks.uiuc.edu/Research/vmd/plugins/saltbr/

其它的盐桥自己写脚本根据原子间距离统计

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[VMD] 如何分析由于N/C端带电而产生的盐桥？