AMBER Archive (2003)

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

From: Junmei Wang (JWang_at_encysive.com)
Date: Tue Nov 11 2003 - 16:33:02 CST

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
>==================================================================
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

= = = = = = = = = = = = = = = = = = = =

Best regards!
Ye Mei
ymei_at_itcc.nju.edu.cn
2003-11-10

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu