AMBER Archive (2004)

Subject: Re: AMBER: How to make leap recognise Zn2+?

From: Yongzhi Chen (yongzhi_mms_at_yahoo.com)
Date: Tue Jul 06 2004 - 11:00:26 CDT

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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