AMBER Archive (2003)

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

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Thu Nov 13 2003 - 00:52:38 CST

Hi,Junmei,

It seems to work correctly.

ATOM 1 C1 PPI 1 -55.549 61.954 0.791
ATOM 2 H1 PPI 1 -55.509 62.708 1.446
ATOM 3 H2 PPI 1 -56.356 61.394 0.978
ATOM 4 H3 PPI 1 -54.727 61.392 0.880
ATOM 5 C2 PPI 1 -55.635 62.515 -0.629
ATOM 6 H4 PPI 1 -56.603 62.580 -0.869
ATOM 7 H5 PPI 1 -55.183 61.862 -1.238
ATOM 8 C3 PPI 1 -54.981 63.882 -0.776
ATOM 9 O1 PPI 1 -53.734 63.955 -0.746
ATOM 10 O2 PPI 1 -55.707 64.890 -0.925
        
And this time I can load the pdb file and build the top and crd file correctly.
Thank you very much.

======= 2003-11-13 04:51:05 =======

>
>
>
>
>
>Hi,
>Would you please try this command:
>antechamber -fi rst -fo pdb -fa ac -i ppi.rst -o ppi.pdb -a ppi.ac
>Please let me know if it does not work.
>
>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
> 11/12/2003 02:48 Re: Re: Re: AMBER: a problem with
> AM antechamber and leap
>
>
> Please respond to
> amber_at_scripps.edu
>
>
>
>
>
>
>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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= = = = = = = = = = = = = = = = = = = =
                        

　　　　　　　
 
Best regards!
Ye Mei
ymei_at_itcc.nju.edu.cn
2003-11-13

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