Dear Amber Users
I used the given command to create a hoogsten base pair for Guanine but the
pdb which is generated does not have the hoogsten base pair but shows a
watson crick base pair. Though the pdb gets generated it shows
title:
default_name
useboundsfrom: atom mismatch:m1(13) & m2(0)
useboundsfrom set bounds for 0 atoms
May I know if there is any mistake with the input.
molecule m;
bounds b;
m = fd_helix( "arna", "g", "rna");
b = newbounds ( m, "ag.1X.pdb");
useboundsfrom(b, m, "1:1,5:??,H?
T]",getpdb("/root/home/Amber12/amber12/dat/dgdb/basepairs/ag.IX.pdb"),"::,H?[
T]",0.1);
useboundsfrom(b, m, "1:2,6:??,H?
T]",getpdb("/root/home/Amber12/amber12/dat/dgdb/basepairs/ga.IX.pdb"),"::,H?[
T]",0.1);
putpdb( "b.pdb", m, "-wwpdb");
The c file :
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include <assert.h>
#include "nabcode.h"
extern char NAB_rsbuf[];
static int mytaskid, numtasks;
static MOLECULE_T *m;
static BOUNDS_T *b;
int main( argc, argv )
int argc;
char *argv[];
{
nabout = stdout; /*default*/
mytaskid=0; numtasks=1;
static STRING_T *__st0001__ = NULL;
static STRING_T *__st0002__ = NULL;
static STRING_T *__st0003__ = NULL;
m = fd_helix( STEMP( __st0001__, "arna" ), STEMP( __st0002__, "g" ), STEMP(
__st0003__, "rna" ) );
b = newbounds( m, "ag.1X.pdb" );
useboundsfrom( b, m, "1:1,5:??,H? T]", getpdb(
"/root/home/Amber12/amber12/dat/dgdb/basepairs/ag.IX.pdb", NULL ), "::,H?[
T]", 1.000000E-01 );
useboundsfrom( b, m, "1:2,6:??,H? T]", getpdb(
"/root/home/Amber12/amber12/dat/dgdb/basepairs/ga.IX.pdb", NULL ), "::,H?[
T]", 1.000000E-01 );
putpdb( "b.pdb", m, "-wwpdb" );
exit( 0 );
}
Is there any error?
I am attaching my pdb file
Thanks in advance
Martina
On Fri, Apr 1, 2016 at 8:53 PM, Martina Devi <martinadevi2011.gmail.com>
wrote:
> Dear Amber Users
>
> I used the given command to create a hoogsten base pair for Guanine but
> the pdb which is generated does not have the hoogsten base pair but shows a
> watson crick base pair. Though the pdb gets generated it shows
>
> title:
> default_name
> useboundsfrom: atom mismatch:m1(13) & m2(0)
> useboundsfrom set bounds for 0 atoms
>
> May I know if there is any mistake with the input.
>
> molecule m;
> bounds b;
>
> m = fd_helix( "arna", "g", "rna");
> b = newbounds ( m, "ag.1X.pdb");
>
> useboundsfrom(b, m, "1:1,5:??,H?
> T]",getpdb("/root/home/Amber12/amber12/dat/dgdb/basepairs/ag.IX.pdb"),"::,H?[
> T]",0.1);
> useboundsfrom(b, m, "1:2,6:??,H?
> T]",getpdb("/root/home/Amber12/amber12/dat/dgdb/basepairs/ga.IX.pdb"),"::,H?[
> T]",0.1);
>
> putpdb( "b.pdb", m, "-wwpdb");
>
> The c file :
>
> #include <stdio.h>
> #include <string.h>
> #include <stdlib.h>
> #include <math.h>
> #include <assert.h>
> #include "nabcode.h"
> extern char NAB_rsbuf[];
> static int mytaskid, numtasks;
>
> static MOLECULE_T *m;
>
> static BOUNDS_T *b;
>
>
> int main( argc, argv )
> int argc;
> char *argv[];
> {
> nabout = stdout; /*default*/
>
> mytaskid=0; numtasks=1;
> static STRING_T *__st0001__ = NULL;
> static STRING_T *__st0002__ = NULL;
> static STRING_T *__st0003__ = NULL;
> m = fd_helix( STEMP( __st0001__, "arna" ), STEMP( __st0002__, "g" ),
> STEMP( __st0003__, "rna" ) );
> b = newbounds( m, "ag.1X.pdb" );
>
> useboundsfrom( b, m, "1:1,5:??,H? T]", getpdb(
> "/root/home/Amber12/amber12/dat/dgdb/basepairs/ag.IX.pdb", NULL ), "::,H?[
> T]", 1.000000E-01 );
> useboundsfrom( b, m, "1:2,6:??,H? T]", getpdb(
> "/root/home/Amber12/amber12/dat/dgdb/basepairs/ga.IX.pdb", NULL ), "::,H?[
> T]", 1.000000E-01 );
>
> putpdb( "b.pdb", m, "-wwpdb" );
>
>
> exit( 0 );
> }
> Is there any error?
>
> Thanks in advance
> Martina
>
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- chemical/x-pdb attachment: b.pdb
Received on Fri Apr 01 2016 - 08:30:06 PDT
