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sunmuer木蟲 (小有名氣)
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[求助]
amber 二硫鍵問題
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我用amber準(zhǔn)備蛋白質(zhì)時(shí) check 說沒有二硫鍵 可是我的pdb 文件是有二硫鍵的呀 SSBOND 1 CYS A 44 CYS A 51 pdb用記事本打開顯示這樣就是有二硫鍵唄 那我接著怎么處理呀 |
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lpxmclt
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In your LEaP input file include: AddPath SIRAH source leaprc.sirah For instance, a typical LEaP file for the protein 1CRN would look like: ✞ ☎ # Load SIRAH force field addPath ./sirah.amber source leaprc.sirah # Load model protein = loadpdb 1CRN_cg.pdb # Info on system charge charge protein # Set S-S bridges bond protein.3.BSG protein.40.BSG bond protein.4.BSG protein.32.BSG bond protein.16.BSG protein.26.BSG # Add solvent, counterions and 0.15M NaCl # Tuned solute-solvent closeness for best hydration solvateOct protein WT4BOX 20 0.7 addIonsRand protein NaW 22 ClW 22 # Save Parms saveAmberParmNetcdf protein 1CRN_cg.prmtop 1CRN_cg.ncrst # EXIT quit ✝ ✆ Notice that three disulfide bonds are created. For this to work, the Cysteine names in your PDB file must be edited from their thiol name (see comment on residue naming below). Thereafter it is just normal Amber stuff! Step-by-step tutorials on different cases of interest can be found in $AMBERHOME/dat/SIRAH/tutorial/. In particular, using input files and initialization protocols contained therein is strongly suggested. Note that the version included in this release corresponds to the version SIRAH 2.1. We recommend users to check and download the latest updates from www.sirahff.com. |
4樓2025-01-09 13:35:30
蘋果變菠蘿
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2樓2012-03-13 19:54:47
lpxmclt
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3樓2025-01-09 13:27:47
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