AMBER Archive (2003)

Subject: AMBER: a problem with antechamber and leap

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Sun Nov 09 2003 - 23:02:04 CST

Hello,everyone£¬

I tried to operate the ligand propionate in a pdb file. First I save the ligand alone in a separated pdb file ppi.pdb, it reads:
ATOM 2059 C3 PPI 133 -55.549 61.954 0.791 1.00 0.00
ATOM 2060 H3 PPI 133 -55.509 62.708 1.446 1.00 0.00
ATOM 2061 H4 PPI 133 -56.356 61.394 0.978 1.00 0.00
ATOM 2062 H5 PPI 133 -54.727 61.392 0.880 1.00 0.00
ATOM 2063 C2 PPI 133 -55.635 62.515 -0.629 1.00 0.00
ATOM 2064 H1 PPI 133 -56.603 62.580 -0.869 1.00 0.00
ATOM 2065 H2 PPI 133 -55.183 61.862 -1.238 1.00 0.00
ATOM 2066 C1 PPI 133 -54.981 63.882 -0.776 1.00 0.00
ATOM 2067 O2 PPI 133 -53.734 63.955 -0.746 1.00 0.00
ATOM 2068 O1 PPI 133 -55.707 64.890 -0.925 1.00 0.00
TER 2069 PPI 133
END

and then ran command "antechamber -i ppi.pdb -fi pdb -o ppi.gjf -fo gcrt -nc -1" to build the gaussian input file, which reads:
#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt

remark line goes here

-1 1
    C -55.5490 61.9540 0.7910
    H -55.5090 62.7080 1.4460
    H -56.3560 61.3940 0.9780
    H -54.7270 61.3920 0.8800
    C -55.6350 62.5150 -0.6290
    H -56.6030 62.5800 -0.8690
    H -55.1830 61.8620 -1.2380
    C -54.9810 63.8820 -0.7760
    O -53.7340 63.9550 -0.7460
    O -55.7070 64.8900 -0.9250

after ab initio calculation, I transfered gout file to prepi file, which reads:
     0 0 2

This is a remark line
PPI.res
PPI XYZ 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 C1 c3 M 3 2 1 1.540 111.208 180.000 -0.102
   5 H1 hc E 4 3 2 1.085 91.954 -126.563 -0.008
   6 H2 hc E 4 3 2 1.092 144.956 0.000 -0.008
   7 H3 hc E 4 3 2 1.085 91.954 126.563 -0.008
   8 C2 c3 M 4 3 2 1.526 33.128 -0.000 0.160
   9 H4 hc E 8 4 3 1.089 110.338 -121.909 -0.097
  10 H5 hc E 8 4 3 1.089 110.338 121.909 -0.097
  11 C3 c M 8 4 3 1.557 115.132 0.000 0.836
  12 O2 o E 11 8 4 1.235 114.222 -180.000 -0.839
  13 O1 o M 11 8 4 1.234 116.298 0.000 -0.839

LOOP

IMPROPER
   C2 O2 C3 O1

DONE
STOP

It seems that no additional information is need after run parmchk.
and run command "tleap -s -f leap.in > leap.out". leap.in reads:
source leaprc.gaff
mods = loadamberparams frcmod
loadamberprep ppi.prepi
lig = loadpdb ppi.pdb
saveamberparm lig lig.top lig.crd
quit

but it seem that leap changed the information between atoms, for the lig.crd reads:

    10
 -54.9810000 63.8820000 -0.7760000 -56.6030000 62.5800000 -0.8690000
 -55.1830000 61.8620000 -1.2380000 -55.5090000 62.7080000 1.4460000
 -55.6350000 62.5150000 -0.6290000 -56.3560000 61.3940000 0.9780000
 -54.7270000 61.3920000 0.8800000 -55.5490000 61.9540000 0.7910000
 -53.7340000 63.9550000 -0.7460000 -55.7070000 64.8900000 -0.9250000
It is in the order:8 6 7 2 5 3 4 1 9 10 in the original pdb file. And the leap.out contains some warning messages:
WARNING: There is a bond of 3.108150 angstroms between:
------- .R<PPI 133>.A<C3 8> and .R<PPI 133>.A<O2 9>
WARNING: There is a bond of 3.404367 angstroms between:
------- .R<PPI 133>.A<C3 8> and .R<PPI 133>.A<O1 10>
WARNING: The unperturbed charge of the unit: -1.002000 is not zero.

Does anyone meet this problem? And how can I solve it?
Thank you.
¡¡¡¡¡¡¡¡¡¡¡¡
                                 
Best regards!
Ye Mei
ymei_at_itcc.nju.edu.cn
2003-11-10
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