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straysme铁虫 (初入文坛)
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[求助]
求助：怎样用ambertools 添加保守水分子。。
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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 |
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