AMBER Archive (2003)

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

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Wed Nov 12 2003 - 02:48:06 CST

Doc. Junmei,
It seems that ppi.rst didn't play any role when running
antechamber -fi ac -fo pdb -i ppi.ac -o ppi.pdb -fa rst -a ppi.rst
the new pdb file contain the recentered coordinates as following:
ATOM 1 C1 PPI 1 1.892 0.086 -0.000
ATOM 2 H1 PPI 1 1.929 0.732 0.871
ATOM 3 H2 PPI 1 2.786 -0.541 -0.000
ATOM 4 H3 PPI 1 1.929 0.732 -0.871
ATOM 5 C2 PPI 1 0.614 -0.748 0.000
ATOM 6 H4 PPI 1 0.592 -1.407 0.867
ATOM 7 H5 PPI 1 0.592 -1.407 -0.867
ATOM 8 C3 PPI 1 -0.710 0.071 0.000
ATOM 9 O1 PPI 1 -0.593 1.299 0.000
ATOM 10 O2 PPI 1 -1.733 -0.620 -0.000
 
        

======= 2003-11-12 06:33:02 =======

>
>
>
>
>
>Hi,
>To solve this problem, you may use the following strategy:
>(1) run antechamber to get the coordinate files
>antechamber -fi pdb -fo rst -i ppi.pdb -o ppi.rst
>(2) run antechamebr to get the gaussian input file
>antechamber -i ppi.pdb -fi pdb -o ppi.gjf -fo gcrt -nc -1
>(3) run gaussian to get gaussian output file
>(4) load gaussian output file and generate an ac file
>antechamber -fi gout -fo ac -i ppi.out -fo ac -i ppi.ac -c resp (you want
>to use resp charge)
>(5) generate ppi.prepi from ppi.ac
>antechamber -fi ac -fo prepi -i ppi.ac -o ppi.prepi
>(6) prepare a new pdb file that combine atom names in ppi.ac and
>coordinates in ppi.rst
>antechamber -fi ac -fo pdb -i ppi.ac -o ppi.pdb -fa rst -a ppi.rst (for
>antechamber in amber7)
>
>With this procedure, you do not need to do any revision on atom names. By
>the way, the sequence order in your new pdb file may be different from that
>of prepi file, but it is OK for leap. The key is to make atom names
>consistant.
>
>
>Best
>
>Junmei
>
>
>===============================================================
>Dr. Junmei Wang
>Chemistry & Biophysics
>Encysive Pharmaceuticals
>7000 Fannin, Houston TX 77030
>Tel: 713-5786649
>Email: jwang_at_tbc.com
>Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
>===============================================================
>
>
>
>
> "Ye Mei"
> <ymei_at_itcc.nju.ed
> u.cn> To
> Sent by: "amber_at_scripps.edu"
> owner-amber_at_scrip <amber_at_scripps.edu>
> ps.edu cc
>
> Subject
> 11/10/2003 03:15 Re: Re: AMBER: a problem with
> AM antechamber and leap
>
>
> Please respond to
> amber_at_scripps.edu
>
>
>
>
>
>
>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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= = = = = = = = = = = = = = = = = = = =
                        

　　　　　　　
 
Best regards!
Ye Mei
ymei_at_itcc.nju.edu.cn
2003-11-12

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