| 查看: 451 | 回复: 0 | |||
straysme铁虫 (初入文坛)
|
[求助]
求助：怎样用ambertools 添加保守水分子。。
|
|
在amber邮件求助中找到：Optionally, you can improve the positions of the hydrogen atoms with pol_h and gwh. Is so, you must put crystal water molecules in a separate file called watpdb, before running leap, and then run leap again with the final result file from gwh. Thus: 1. Move crystal waters to a separate file wat.pdb 2. Run tleap as above, but do not set pdbwritecharges, do not solvate and do not check: x=loadpdb pdb_file bond x.22.SG x.65.SG savepdb x pdbout saveamberparm x prmtop prmcrd quit 3. Run pol_h (it gives the position of the polar hydrogens, but not on water molecules): pol_h ppdbout This usually takes ~1 minute. This is the protonated file for the protein. Add a proper title to this file (a row starting with REMARK) 4. Convert the prmtop file to old format: new2oldparm prmtop.old 5. Run gwh (it calculates improved positions of the water hydrogens) gwh -w wat.pdb -elstat -p prmtop.old wpdb It usually takes about 5 minutes, and it may crash. Add this file to the protonated pdb file: cat wpdb >> ppdbout remove then END record before the water molecules 但是找不到pol_h and gwh 这两个程序。求各路大神帮助。。。谢谢@smutao@oxox6085@oxox6085@oxox6085 |
回复此楼» 猜你喜欢
投稿返修后收到这样的回复，还有希望吗
已经有7人回复
-
压汞仪和BET测气凝胶孔隙率
已经有4人回复
-
博士申请都是内定的吗？
已经有14人回复
-
博士申请
已经有3人回复
-
谈谈两天一夜的“延安行”
已经有13人回复
-
氨基封端PDMS和HDI反应快速固化
已经有11人回复
-
之前让一硕士生水了7个发明专利，现在这7个获批发明专利的维护费可从哪儿支出哈？
已经有11人回复
-
论文投稿求助
已经有4人回复
-
Applied Surface Science 这个期刊。有哪位虫友投过的能把word模板发给我参考一下嘛
已经有3人回复
-
投稿精细化工
已经有6人回复
» 本主题相关商家推荐: (我也要在这里推广)
