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[求助] amber 二硫键问题

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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出清水而不染

1楼2012-03-05 11:08:43

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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.