Na

show sticks, resn MOL
select ion_test, inorganic
show spheres, ion_test
set sphere_scale, 0.5, ion_test


label sele, "Na 302"
set float_labels,1

Step 0：准备干燥轨迹

# 建索引文件（蛋白+配体+Na+）gmx_mpi make_ndx -f ../../md.gro -o protein_na_lig.ndx# 输入：1|13|14 → q# 提取干燥轨迹gmx_mpi trjconv \    -f ../../md.xtc \    -s ../../md.tpr \    -n protein_na_lig.ndx \    -o dry-na.xtc \    -pbc mol -ur compact# 选择：18 (Protein_MOL_Na+)

Step 1：建native_na.prmtop

# 从complex.prmtop去掉水cpptraj << 'EOF'parm ../../../parameters/complex.prmtopparmstrip :WATparmwrite out native_na.prmtopquitEOF

Step 2：对齐轨迹

cpptraj << 'EOF'parm native_na.prmtoptrajin dry-na.xtcautoimagerms first :1-291@CAtrajout dry-na-align.xtcrunquitEOF
cpptraj << 'EOF'
parm native_na.prmtop
trajin dry-na.xtc
autoimage
rms first :1-291@CA
trajout dry-na-align.xtc
run
quit
EOF

Step 3：抽帧检查

cpptraj << EOF
parm native_na.prmtop
trajin dry-na-align.xtc 1 10000000000 1000
trajout check.pdb
run
quit
EOF

Step 4：找最近Na+

# 计算所有Na+到配体距离（300-500ns）cpptraj << 'EOF'parm native_na.prmtoptrajin dry-na-align.xtc 150001 250001 1000distance na293 :293 :292 out dist_na.datdistance na294 :294 :292 out dist_na.datdistance na295 :295 :292 out dist_na.datdistance na296 :296 :292 out dist_na.datdistance na297 :297 :292 out dist_na.datdistance na298 :298 :292 out dist_na.datdistance na299 :299 :292 out dist_na.datdistance na300 :300 :292 out dist_na.datdistance na301 :301 :292 out dist_na.datdistance na302 :302 :292 out dist_na.datdistance na303 :303 :292 out dist_na.datdistance na304 :304 :292 out dist_na.datdistance na305 :305 :292 out dist_na.datdistance na306 :306 :292 out dist_na.datdistance na307 :307 :292 out dist_na.datdistance na308 :308 :292 out dist_na.datdistance na309 :309 :292 out dist_na.datdistance na310 :310 :292 out dist_na.datdistance na311 :311 :292 out dist_na.datrunquitEOF# 排序awk 'NR==1{next} {for(i=2;i<=NF;i++) sum[i]+=$i; count++} \    END{for(i=2;i<=NF;i++) printf "Na%d\t%.2f Å\n", i+291, sum[i]/count}' \    dist_na.dat | sort -k2 -n | head -5

Step 5：建prmtop（以Na302为例）

mkdir na302# native（蛋白+Na302+配体）cpptraj << 'EOF'parm ../../../parameters/complex.prmtopparmstrip :WATparmstrip :293-301,303-311parminfoparmwrite out na302/native_na302.prmtopquitEOF# pro两步法（蛋白+Na302）cpptraj << 'EOF'parm ../../../parameters/complex.prmtopparmstrip :WATparmstrip :MOLparmstrip :293-301parmwrite out na302/pro_na302_temp.prmtopquitEOFcpptraj << 'EOF'parm na302/pro_na302_temp.prmtopparmstrip :Na+&!:292parminfoparmwrite out na302/pro_na302.prmtopquitEOFrm na302/pro_na302_temp.prmtop# 验证 native = pro + lig# 4672 + 127 = 4799 ✅

Step 6：提取Na302轨迹

cpptraj << 'EOF'parm native_na.prmtoptrajin dry-na-align.xtcstrip :293-301,303-311trajout na302/dry-na302-align.xtcrunquitEOF# 抽帧检查cpptraj << 'EOF'parm na302/native_na302.prmtoptrajin na302/dry-na302-align.xtc 1 10000000000 1000trajout na302/check_na302.pdbrunquitEOF

Step 7：跑MMGBSA

cd ../MMGBSA-NA/mkdir na302cp /path/to/igb5_300-500ns.in na302/cd na302nohup mpirun -np 20 MMPBSA.py.MPI \    -i igb5_300-500ns.in \    -o final_na302.dat \    -cp ../../RMSD-NA/na302/native_na302.prmtop \    -rp ../../RMSD-NA/na302/pro_na302.prmtop \    -lp ../../../../parameters/lig.prmtop \    -y ../../RMSD-NA/na302/dry-na302-align.xtc \    -eo mmgbsa_na302.csv > mmpbsa_na302.log 2>&1 &echo "PID: $!"# 查看结果grep "DELTA TOTAL" final_na302.dat

注意事项

:292         → 配体MOL编号（根据实际确认）:293-311     → 19个Na+编号（根据实际确认）两步法建pro  → 因cpptraj strip后残基重新编号cp=rp+lp    → 原子数必须匹配否则MMGBSA报错300-500ns   → 对应帧150001-250001（每2ps一帧）native_na.prmtop → 所有md共用（同一parameters）