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[求助]
amber 二硫键问题
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我用amber准备蛋白质时 check 说没有二硫键 可是我的pdb 文件是有二硫键的呀 SSBOND 1 CYS A 44 CYS A 51 pdb用记事本打开显示这样就是有二硫键呗 那我接着怎么处理呀 |
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2楼2012-03-13 19:54:47
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3楼2025-01-09 13:27:47
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楼2025-01-09 13:35:30
