Dear NAB-users,
I am trying to create a Hoogsteen base pair A2:T5 in 5'-AAA-3' B-DNA
structure using "useboundsfrom" option in NAB. I have tried to create DNA
duplex using following NAB script:
#################################
molecule m;
bounds b;
float fret, xyz[ dynamic ];
int ier;
string opt;
m = fd_helix( "abdna","aaa","dna");
b = newbounds ( m, "");
allocate xyz[ 4*m.natoms ];
//Creating Hoogsteen A:T base pair in the middle of "AAA" sequence
useboundsfrom(b, m,"1:2:??,H?",getpdb( "$AMBERHOME/dat/dgdb/basepairs/" +
"at.XXIII.pdb" ),"::", 0.1 );
useboundsfrom(b, m,"2:5:??,H?",getpdb( "$AMBERHOME/dat/dgdb/basepairs/" +
"at.XXIII.pdb" ),"::", 0.1 );
tsmooth(b, 0.0005);
opt = "seed=-1, gdist=0, ntpr=50, k4d=1.0, kchi=1.0, randpair=5, pembed=1,
rbox=100, riter=250000";
dg_options( b, opt );
embed(b, xyz );
ier = conjgrad( xyz, 4*m.natoms, fret, db_viol, 0.1, 10., 2000000 );
printf( "conjgrad returns %d\\n", ier );
setmol_from_xyzw( m, NULL, xyz );
putpdb( "new.pdb", m );
#################################
However, I am experiencing 2 problems :
1) first, I am getting atom mismatch warning (useboundsfrom: atom mismatch:
m1(12) & m2(64) useboundsfrom: atom mismatch: m1(0) & m2(64)) and ;
2) the generated PDB file "new.pdb" has 6 residues dispersed in the vacuum.
When I used above script for single A:T base pair, it works fine, however
generating a deformed Hoogsteen base pair.
Any guidance or expert's comments, in this case, will be really helpful.
Thanks in advance.
Best Regards,
Mandar Kulkarni
Postdoctoral Research Fellow,
Department of Chemistry,
Pusan National University,
Busan, South Korea
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 19 2017 - 03:00:02 PDT
