AMBER Archive (2003)

Subject: Re: Re: AMBER: a problem with antechamber and leap

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Mon Nov 10 2003 - 03:15:06 CST

Dear David,

Your input file do works, but I cannot judge whether it is correct or nor, for in ppi.prepi file the coordinates are in z-mat format, but in the lig.crd are in Cartesian format.
Moreover, I don't know whether amber change the order of other properties, like mass, charge, etc.

======= 2003-11-10 15:24:41 =======

>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
>
>--
>
>==================================================================
>David A. Case | e-mail: case_at_scripps.edu
>Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
>The Scripps Research Institute | phone: +1-858-784-9768
>10550 N. Torrey Pines Rd. | home page:
>La Jolla CA 92037 USA | http://www.scripps.edu/case
>==================================================================
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Best regards!
Ye Mei
ymei_at_itcc.nju.edu.cn
2003-11-10

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