Dear Guanglei:
Yes. I could find the following information:
$ grep -iw zn parm*.dat
parm99.dat:Zn 65.4 Zn2+
parm99.dat: Zn 1.10 0.0125 Zn2+, Merz,PAK, JACS,113,
8262,(1991)
parm99EP.dat:Zn 65.4 Zn2+
parm99EP.dat: Zn 1.10 0.0125 Zn2+, Merz,PAK, JACS,113
,8262,(1991)
But what should I do next? When I use the command:
tleap ¨Cf $AMBERHOME/dat/leap/cmd/leaprc.ff99
parm99.dat is loaded into tleap, but Zn in not in the list. If I directly load
the 3BTA.pdb, I will got
> mol = loadpdb 3BTA.pdb
Loading PDB file: ./3BTA.pdb
Unknown residue: ZN number: 1277 type: Terminal/last
...relaxing end constraints to try for a dbase match
-no luck
If I repeat the following procedure
> i = createAtom ZN ZN 2.0
position { 0 0 0 }
r = createResidue ZN
> set i element Zn
r
saveOff ZN ./Zn.off
> set i position { 0 0 0 }
> r = createResidue ZN
> add r i
> ZN = createUnit ZN
> add ZN r
> saveOff ZN ./Zn.off
Creating ./Zn.off
Building topology.
Building atom parameters.
Tleap will not complain when it is loaded the 3BTA.pdb but I will meet the
same problem:
For atom: .R<ZN 1278>.A<ZN 1> Could not find type: ZN
Parameter file was not saved.
Could you give me further direction? Thanks a lot.
Yongzhi
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Received on Tue Jul 06 2004 - 17:53:01 PDT
