Dear Dr. Jason,
At first, I used reduce with trim command as
reduce -trim filename > new_filename # input file is
filename and output file is new_filename
Then, I used reduce with build command as
reduce -build new_filename > final_filename # input file is
new_filename and output file is final_filename
When I used tleap command directly without using these
reduce and trim, H-atoms got added in the file. The problem mentioned in
the previous mail only appeared when used reduce command. As mentioned in
the amber tutorial A1, I had removed connectivities and headers from the
pdb file before applying the reduce command.
Thank you for the help,
Mahendra Thapa
On Fri, Apr 13, 2012 at 6:26 PM, Thapa, Mahendra (thapamb) <
thapamb.mail.uc.edu> wrote:
>
>
>
> ________________________________________
> From: Jason Swails
> Sent: Friday, April 13, 2012 4:25:01 PM (UTC-06:00) Central America
> To: AMBER Mailing List
> Subject: Re: [AMBER] reduce and trim function
>
> What exact reduce commands did you use?
>
> On Fri, Apr 13, 2012 at 12:17 PM, Mahendra B Thapa <thapamb.mail.uc.edu
> >wrote:
>
> > Dear Amber users
> >
> > Atom number of a pdb [ 2nd column ] is not continuous
> > after using trim and reduce of AMBER command , instead " new" appears in
> > the last column. May I have to use some programs ( like perl ) to get
> > continuous as just before using the trim and reduce?
> >
> > *Before* using " trim and then reduce" command of AMBER ( a portion of
> PDB)
> > ATOM 1 N MET A 0 2.087 8.287 -1.145 1.00
> > 29.31 N
> > ATOM 2 CA MET A 0 1.516 9.645 -0.899 1.00
> > 28.06 C
> > ATOM 3 C MET A 0 2.162 10.704 -1.788 1.00
> > 27.19 C
> > ATOM 4 O MET A 0 1.619 11.752 -2.238 1.00
> > 26.90 O
> > ATOM 5 CB MET A 0 1.819 9.901 0.601 1.00
> > 31.06 C
> > ATOM 6 N LYS A 1 3.440 10.436 -2.034 1.00
> > 24.33 N
> > ATOM 7 CA LYS A 1 4.326 11.276 -2.844 1.00
> > 22.35 C
> > ATOM 8 C LYS A 1 5.166 10.393 -3.771 1.00
> > 20.85 C
> > ATOM 9 O LYS A 1 5.580 9.289 -3.327 1.00
> > 20.59 O
> > ATOM 10 CB LYS A 1 5.252 12.085 -1.921 1.00
> > 22.60 C
> > ATOM 11 CG LYS A 1 4.400 13.116 -1.143 1.00
> > 24.98 C
> > ATOM 12 CD LYS A 1 5.237 13.720 -0.049 1.00
> > 27.59 C
> > ATOM 13 CE LYS A 1 4.283 14.413 0.937 1.00
> > 29.67 C
> > ATOM 14 NZ LYS A 1 3.765 15.649 0.280 1.00
> > 30.63 N
> >
> >
> >
> > *After* using at first "trim" and then " reduce" command of AMBER ( a
> > portion of PDB)
> > ATOM 1 N MET A 0 2.087 8.287 -1.145 1.00
> > 29.31 N
> > ATOM 2 CA MET A 0 1.516 9.645 -0.899 1.00
> > 28.06 C
> > ATOM 3 C MET A 0 2.162 10.704 -1.788 1.00
> > 27.19 C
> > ATOM 4 O MET A 0 1.619 11.752 -2.238 1.00
> > 26.90 O
> > ATOM 5 CB MET A 0 1.819 9.901 0.601 1.00
> > 31.06 C
> > ATOM 0 H1 MET A 0 1.458 7.592 -0.796 1.00
> > 29.31 H new
> > ATOM 0 H2 MET A 0 2.220 8.154 -2.127 1.00
> > 29.31 H new
> > ATOM 0 H3 MET A 0 2.967 8.205 -0.676 1.00
> > 29.31 H new
> > ATOM 0 HA MET A 0 0.443 9.699 -1.134 1.00
> > 28.06 H new
> > ATOM 6 N LYS A 1 3.440 10.436 -2.034 1.00
> > 24.33 N
> > ATOM 7 CA LYS A 1 4.326 11.276 -2.844 1.00
> > 22.35 C
> >
> > Thanks ,
> > Mahendra Thapa
> > University of Cincinnati
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Sun Apr 15 2012 - 15:00:03 PDT
