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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Received on Fri Apr 01 2016 - 08:30:05 PDT
