Hi, Amber:
I have a question regarding to prepare the parameter files with tleap.
My goal is inputting 3BTA.pdb to tleap and getting the corresponding 3BTA..prmtop and 3BTA.inpcrd. The last atom in 3BTA.pdb is a heterogen atom, Zn2+ and it is not in the tleap template. Therefore I need to give the description to the tleap. I followed the commands in ions94.cmd that define the Mg2+:
> i = createAtom ZN ZN 2.0
{ 0 0 0 }
r = createResidue ZN
add r i
> set i element Zn
> set i position { 0 0 0 }
> r = createResidue ZN
> add r i
> ZN = createUnit ZN
> add ZN r
> saveOff ZN ./ions94.lib
Creating ./ions94.lib
Building topology.
Building atom parameters.
> list
ACE ALA ARG ASH ASN ASP CALA CARG
CASN CASP CCYS CCYX CGLN CGLU CGLY CHCL3BOX
CHID CHIE CHIP CHIS CILE CIO CLEU CLYS
CMET CPHE CPRO CSER CTHR CTRP CTYR CVAL
CYM CYS CYX Cl- Cs+ DA DA3 DA5
DAN DC DC3 DC4 DC5 DCN DG DG3
DG5 DGN DT DT3 DT5 DTN GLH GLN
GLU GLY HID HIE HIP HIS HOH IB
ILE K+ LEU LYN LYS Li+ MEOHBOX MET
MG2 NALA NARG NASN NASP NCYS NCYX NGLN
NGLU NGLY NHE NHID NHIE NHIP NHIS NILE
NLEU NLYS NMABOX NME NMET NPHE NPRO NSER
NTHR NTRP NTYR NVAL Na+ PHE PL3 POL3BOX
PRO RA RA3 RA5 RAN RC RC3 RC5
RCN RG RG3 RG5 RGN RU RU3 RU5
RUN Rb+ SER SPC SPCBOX T4E THR TIP3PBOX
TIP4PBOX TIP4PEWBOXTP3 TP4 TP5 TRP TYR VAL
WAT ZN frcmod03 i parm99 r
I guess I already successfully added the description of Zn2+ into the ion library since it is in the list now and there is no warning or error when I loaded 3BTA.pdb into tleap. But when I tried to generate the parameter files I met the following error:
> saveAmberParm mol 3bta.prmtop 3bta.inpcrd
Checking Unit.
WARNING: There is a bond of 9.735295 angstroms between:
------- .R<ARG 431>.A<C 23> and .R<ASN 432>.A<N 1>
-- ignoring the warning.
Building topology.
Building atom parameters.
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.
Another thing I worried about happened in residue 431 and 450. From the remarks in the 3BTA.pdb, I known that residue 432-449 were not located in the experiment and the residue 431 have missing atoms CG CD NE CZ NH1 NH2 and residue 450 have missing atoms CG OD1 ND2. As I already found, when I loaded the 3BTA.pdb into tleap. Tleap would add these missing atoms automatically. As I understood, this protein is a di-chain one linked by a disulfide bond (residue 429-residue453). In this case, should I add a ¡°TER¡± cards between the residue 431 and residue 450 lines? I found if I do in that way, tleap would add one more atom OXT. Which method is right?
Yongzhi
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- application/x-zip-compressed attachment: 3BTA.zip
Received on Tue Jul 06 2004 - 03:53:00 PDT
