求助：用Dynamical Network Analysis节点怎么设置？

hyr95

>Dcds
../1.network preparation/gluRStRNA.dcd
>SystemSelection
(chain P N X) and (not hydrogen)
>NodeSelection
(name CA P) or (resname CYT URA and name N1) or (resname ADE GUA GOM
and name N9)
>Clusters
N9 ADE name N9 C8 N7 C5 C6 N6 N1 C2 N3 C4
P ADE name P O1P O2P O5’ C5’ C4’ O4’ C1’ C3’ C2’ O2’ O3’
N1 CYT name N1 C2 O2 N3 C4 N4 C5 C6
P CYT name P O1P O2P O5’ C5’ C4’ O4’ C1’ C3’ C2’ O2’ O3’
N9 GUA name N9 C8 N7 C5 C6 O6 N1 C2 N2 N3 C4
P GUA name P O1P O2P O5’ C5’ C4’ O4’ C1’ C3’ C2’ O2’ O3’
N1 URA name N1 C6 C5 C4 O4 N3 C2 O2
P URA name P O1P O2P O5’ C5’ C4’ O4’ C1’ C3’ C2’ O2’ O3’
P GOM name P O1P O2P O3P O5’ C5’ C4’ O4’ C1’ C3’ C2’ O2’ O3’
CA GOM name N CA CB CG CD OE1 OE2 C O
>Restrictions
notSameResidue
notNeighboringCAlpha
notNeighboringPhosphate



我准备用Dynamical Network Analysis分析跑完md的蛋白构象变化，请问这个脚本里设置的内容是什么意思呀？NodeSelection和Clusters怎么设置呀？

xking

楼主，现在的网络模型，节点设置解决了吗

hyr95

xking 发表于 2021-7-22 16:01
楼主，现在的网络模型，节点设置解决了吗

没有 我现在已经不做这个了