Thanks for your suggestions.
My problem is still not resolved. I used antechamber to create the file
bz.prepin as shown below
0 0 2
This is a remark line
molecule.res
1 INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 C CA M 3 2 1 1.540 111.208 180.000 0.00000
5 H1 HA E 4 3 2 1.086 29.987 90.000 0.00000
6 C1 CA M 4 3 2 1.397 90.000 -90.000 0.00000
7 H5 HA E 6 4 3 1.086 119.987 -0.000 0.00000
8 C2 CA M 6 4 3 1.397 119.979 -180.000 0.00000
9 H4 HA E 8 6 4 1.087 119.926 180.000 0.00000
10 C3 CA M 8 6 4 1.397 119.986 0.000 0.00000
11 H3 HA E 10 8 6 1.087 119.932 180.000 0.00000
12 C4 CA M 10 8 6 1.396 120.035 0.000 0.00000
13 H2 HA E 12 10 8 1.086 119.987 180.000 0.00000
14 C5 CA M 12 10 8 1.397 119.979 0.000 0.00000
15 H HA E 14 12 10 1.087 119.979 180.000 0.00000
LOOP
C5 C
IMPROPER
C5 C1 C H1
C C2 C1 H5
C1 C3 C2 H4
C4 C2 C3 H3
C5 C3 C4 H2
C4 C C5 H
DONE
STOP
The commands given out are as follows:
tleap
source leaprc.ff99
BZ=loadAmberPrep bz.prepin
after this command, the message that came is <Loading Prep file:
./bz.prepin>
then I gave the command
saveAmberParm BZ prmtop prmcrd
after this came
saveAmberParm: Argument #1 is type String must be of type: [unit]
usage: saveAmberParm <unit> <topologyfile> <coordfile>
I think I now have a unit called BZ, but on typing list, all I found is
1 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 SPCFWBOX
SPF
T4E THR TIP3PBOX TIP4PBOX TIP4PEWBOXTP3 TP4
TP5
TRP TYR VAL WAT parm99
no listing of my BZ as a unit.
I would appreciate if the error could be pointed out to me.
Johnson Agbo
cccccccccccccccccccccccccc
6060 Silver Lake Road #8D
Reno, NV 89506
775-971-1914
cccccccccccccccccccccccccc
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Received on Wed Jul 11 2007 - 06:07:48 PDT
