个人觉得默认的do_dssp绘图出来的并不好看,还需要自行ps处理,查看了一下原来第二步xpm2ps的时候可以进行设置,具体可以看官方说明.自己捣鼓了一下发现m2p的输入文件如下设置比较美观:

m2p-m2p:

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; Command line options of xpm2ps override the parameters in this file
black&white = no                                ; Obsolete
titlefont = Times-Roman                     ; A PostScript Font
titlefontsize = 42                                  ; Font size (pt)
legend = yes                                         ; Show the legend
legendfont = Times-Roman                 ; A PostScript Font
legendlabel =                                        ; Used when there is none in the .xpm
legend2label =                                      ; Used when merging two xpm’s
legendfontsize = 36                              ; Font size (pt)
xbox = 2.0                                             ; x-size of a matrix element
ybox = 2.0                                             ; y-size of a matrix element
matrixspacing = 2.0                              ; Space between 2 matrices
xoffset = 0.0                                          ; Between matrix and bounding box
yoffset = 0.0                                          ; Between matrix and bounding box
x-major = 20000                                   ; Major ticks on x axis every .. frames
x-minor = 5                                           ; Id. Minor ticks
x-firstmajor = 0                                     ; First frame for major tick
x-majorat0 = no                                    ; Major tick at first frame
x-majorticklen = 8.0                              ; x-majorticklength
x-minorticklen = 4.0                             ; x-minorticklength
x-label =                                                ; Used when there is none in the .xpm
x-fontsize = 36                                      ; Font size (pt)
x-font = Times-Roman                         ; A PostScript Font
x-tickfontsize = 30                               ; Font size (pt)
x-tickfont = Helvetica                          ; A PostScript Font
y-major = 20
y-minor = 5
y-firstmajor = 0
y-majorat0 = no
y-majorticklen = 8.0
y-minorticklen = 4.0
y-label =
y-fontsize = 36
y-font = Times-Roman
y-tickfontsize = 30
y-tickfont = Helvetica

dssp-sh如下:

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#!/bin/bash
# author:kangsgo
# method:
# loop 后面为文件夹变量,表示进入哪个文件夹
# trj_125-150ns.xtc 轨迹变量
for loop in achmd bnf318 qna tcdd
do
echo “开始运行”
cp m2p.m2p /home/gromacs/shiyan/$loop
cd /home/gromacs/shiyan/$loop
do_dssp -f md200skip.xtc -s npt.tpr -n index.ndx -o fwss.xpm
xpm2ps -f fwss.xpm -o fwss.eps -by 2 -bx 1 -di m2p.m2p
convert fwss.eps $loop.bmp
done