Date: Sun, 9 Nov 2003 23:24:41 -0800
From: "David A. Case"
Subject: Re: AMBER: a problem with antechamber and leap

On Mon, Nov 10, 2003, Ye Mei wrote:
>
> 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.
>

Yes, this is a bit of a problem, that Junmei and I need to think about. Two
somewhat independent things are going on here:

When antechamber creates the prepi file, the order of atoms is not guaranteed
to be the same as in the original pdb file. Rather, following a
long-standing (if not necessarily optimal) Amber tradition, it creates it in a
tree-format, as you saw. This means that you must either (a) re-organize your
pdb file to match the prepi order; or (b, probably easier) avoid the "loadpdb"
statement above, and just use the coordinates in the prepi file. What you
cannot do (as you found) is load both the prepi file and the un-modified pdb
file, since they have different and incompatible atom orders.

In suggestion (b), this would become your input file:

source leaprc.gaff
mods = loadamberparams frcmod
loadamberprep ppi.prepi
saveamberparm PPI lig.top lig.crd
quit

See if this works for you.

[This, by the way, is yet another reason why I think the prepi format should
be deprecated in the next version, in favor of the mol2 format.]

The second thing that happened here is something that I had not known before:
in making the Gaussian input file, the atom names were truncated down to a
single letter (which is really not necessary). Then, antechamber recreated
these numbers later on to make all of the atom names unique. This has the
effect that the atom names also got changed from your original input, which
should not be happening, and can be extremely confusing. Again, I think
that avoiding the prepi format will also fix this problem, but we'll have to
check into that.

..thanks for your report....hope this helps...dac