you should check the residue numbers that leap is using for the Cys- it is
not the same as the original pdb. use the "desc" command to check things.
details for that are in the manual.
2010/3/31 xuemeiwang1103 <xuemeiwang1103.163.com>
> Hi:
> I am modeling a protein with 3 disulfide
> bonds(cys152-cys158,cys352-cys370,cys538-cys550).Following the manual ,I
> have changd the CYS to CYX and done the "bond"comand.The strange thing
> happaned when I used the bond comand,the comand "bond 1oaa.152.SG
> 1oaa.158.SG"and "bond 1oaa.352.SG 1oaa.370.SG" worked ok ,but when I used
> the third comand"bond 1oaa.538.SG 1oaa.550.SG",it displays"bond: Argument
> #1 is type String must be of type: [atom]",How strange is it ! Could someone
> tell me the reason? BTW,my original pdb is began from HiS 40 ,and it missing
> several residues,.I have changed the residues numbers ,but by doing this
> ,all the "bond"comand didn't work!
> tleap :
> > tleap -s -f leaprc.ff99
> > 1oaa=loadpdb 1oaa.pdb
> > bond 1oaa.152.SG 1oaa.158.SG
> >bond 1oaa.352.SG 1oaa.370.SG
> >bond 1oaa.538.SG 1oaa.550.SG
> bond: Argument #1 is type String must be of type: [atom]
> usage: bond <atom1> <atom2> [order]
>
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Received on Wed Mar 31 2010 - 07:00:08 PDT
