Re: [AMBER] Creating hoogsteen basepaired DNA using NAB

From: Andre Serobian <a.serobian.unsw.edu.au>
Date: Fri, 22 Jul 2011 14:26:26 +1000

Dear David,

Thankyou for the advice. The program is now presenting a the error below:

nab file:
..............................................................................................................................
molecule m;
molecule m1;
molecule m2;
bounds b;
string seq, cseq;
float fret, xyz[ 10000 ];
int ier;

seq = "atgcat";
cseq = wc_complement( "atgcat", "", "dna" );
m = wc_helix( seq, "", "dna", cseq, "", "dna", 2.25, -4.96, 36.0, 3.38, "" );
b = newbounds ( m, "");
m1 = getpdb("/usr/local/amber11.1/dat/dgdb/basepairs/at.XXIII.pdb");
m2 = getpdb("/usr/local/amber11.1/dat/dgdb/basepairs/ta.XXIII.pdb");

useboundsfrom(b, m, "1:1,5:??,H?[T]",m1,"::??,H?[T]",0.1);
useboundsfrom(b, m, "1:2,6:??,H?[T]",m2,"::??,H?[T]",0.1);
tsmooth(b, 0.0005);

dg_options( b, "gdist=1, ntpr=50, k4d=2.0, randpair=10.0" );
embed( b, xyz );
ier = conjgrad( xyz, 4*m.natoms, fret, db_viol, 0.1, 10.0, 500 );
setmol_from_xyzw( m, NULL, xyz );
putpdb( "atgcat-hoog.pdb", m, "-wwpdb" );
..............................................................................................................................



error message:
..............................................................................................................................
useboundsfrom: atom mismatch: m1(24) & m2(23)
useboundsfrom: atom mismatch: m1(22) & m2(23)
        dg_options: gdist=1
        dg_options: ntpr=50
        dg_options: k4d=2.0
        dg_options: randpair=10.0
embed attempt 1
random metrization for 7277 pairs
average bounds gap = 1.617
eigenvector 1: 3835597628.265 iter: 5
eigenvector 2: 52389445.454 iter: 7
eigenvector 3: -28514074.437 iter: 86

embed attempt 2
random metrization for 7277 pairs
average bounds gap = 1.757
eigenvector 1: 995904893.310 iter: 5
eigenvector 2: 13697623.891 iter: 5
eigenvector 3: 7801563.181 iter: 400

Segmentation fault
..............................................................................................................................


Does this mean it does not recognise how to connect the inserted bases?

Kind regards,

Andre



________________________________________
From: case [case.biomaps.rutgers.edu]
Sent: Saturday, 9 July 2011 1:08 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Creating hoogsteen basepaired DNA using NAB

On Sat, Jul 09, 2011, Andre Serobian wrote:
>
> useboundsfrom(b, m, "1:1,5:??,H?T]",getpdb( /usr/local/amber11/dat/dgdb/basepairs + "at.XXIII.pdb" ),"::??,H?[T]",0.1);

You have to put quotes around the /usr/local/amber....pairs argument to
getpdb. Also, the first atom expression is garbled, looks like perhaps a
missing "[". The example in the book has a very complex atom expression --
you should either figure out what everything means, and/or start with simpler
expressions.

Note that simplifying things in other ways can be a good debugging option,
e.g.

molecule m1;
m1 = getpdb( ....);

Then use m1 as the fourth argument to useboundsfrom();

Tracking down errors like this often takes a lot of divide and conquer work.

....dac


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Received on Thu Jul 21 2011 - 22:00:02 PDT
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