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From: Kevin Hauser <84hauser.gmail.com>

Date: Sun, 27 Jun 2010 12:56:03 -0400

Hi, Monica,

Once you built the DNA with NAB, did you load the output PDB into

visualization program, like Chimera, or VMD, and then re-save the PDB before

loading it into leap?

It's weird that only the hydrogen atom names are the problem. Usually,

visualization programs like Chimera, or VMD, etc., have their own hydrogen

atom naming conventions, which are usually NOT acceptable by AMBER (leap,

that is).

-kevin

On Sun, Jun 27, 2010 at 12:50 AM, <monica.imtech.res.in> wrote:

*> sir '
*

*> i already sent the pdb file in earlier mail and after loading into
*

*> leaprc.ff99SB,i got following messege:
*

*> dna1 = loadpdb oligo_p.pdb
*

*> Loading PDB file: ./oligo_p.pdb
*

*> Created a new atom named: HO5' within residue: .R<DG 1>
*

*> Created a new atom named: H5' within residue: .R<DG 1>
*

*> Created a new atom named: H5'' within residue: .R<DG 1>
*

*> Created a new atom named: H2' within residue: .R<DG 1>
*

*> Created a new atom named: H2'' within residue: .R<DG 1>
*

*> Added missing heavy atom: .R<DG 1>.A<P 1>
*

*> Added missing heavy atom: .R<DG 1>.A<O1P 2>
*

*> Added missing heavy atom: .R<DG 1>.A<O2P 3>
*

*> Created a new atom named: H5' within residue: .R<DG 2>
*

*> Created a new atom named: H5'' within residue: .R<DG 2>
*

*> Created a new atom named: H2' within residue: .R<DG 2>
*

*> Created a new atom named: H2'' within residue: .R<DG 2>
*

*> Created a new atom named: H5' within residue: .R<DT 3>
*

*> Created a new atom named: H5'' within residue: .R<DT 3>
*

*> Created a new atom named: H2' within residue: .R<DT 3>
*

*> Created a new atom named: H2'' within residue: .R<DT 3>
*

*> Created a new atom named: H5' within residue: .R<DT 4>
*

*> Created a new atom named: H5'' within residue: .R<DT 4>
*

*> Created a new atom named: H2' within residue: .R<DT 4>
*

*> Created a new atom named: H2'' within residue: .R<DT 4>
*

*> Created a new atom named: H5' within residue: .R<DT 5>
*

*> Created a new atom named: H5'' within residue: .R<DT 5>
*

*> Created a new atom named: H2' within residue: .R<DT 5>
*

*> Created a new atom named: H2'' within residue: .R<DT 5>
*

*> Created a new atom named: H5' within residue: .R<DA 6>
*

*> Created a new atom named: H5'' within residue: .R<DA 6>
*

*> Created a new atom named: H2' within residue: .R<DA 6>
*

*> Created a new atom named: H2'' within residue: .R<DA 6>
*

*> Created a new atom named: H5' within residue: .R<DT 7>
*

*> Created a new atom named: H5'' within residue: .R<DT 7>
*

*> Created a new atom named: H2' within residue: .R<DT 7>
*

*> Created a new atom named: H2'' within residue: .R<DT 7>
*

*> Created a new atom named: H5' within residue: .R<DT 8>
*

*> Created a new atom named: H5'' within residue: .R<DT 8>
*

*> Created a new atom named: H2' within residue: .R<DT 8>
*

*> Created a new atom named: H2'' within residue: .R<DT 8>
*

*> Created a new atom named: H5' within residue: .R<DA 9>
*

*> Created a new atom named: H5'' within residue: .R<DA 9>
*

*> Created a new atom named: H2' within residue: .R<DA 9>
*

*> Created a new atom named: H2'' within residue: .R<DA 9>
*

*> Created a new atom named: H5' within residue: .R<DA 10>
*

*> Created a new atom named: H5'' within residue: .R<DA 10>
*

*> Created a new atom named: H2' within residue: .R<DA 10>
*

*> Created a new atom named: H2'' within residue: .R<DA 10>
*

*> Created a new atom named: H5' within residue: .R<DC 11>
*

*> Created a new atom named: H5'' within residue: .R<DC 11>
*

*> Created a new atom named: H2' within residue: .R<DC 11>
*

*> Created a new atom named: H2'' within residue: .R<DC 11>
*

*> Created a new atom named: H5' within residue: .R<DT 12>
*

*> Created a new atom named: H5'' within residue: .R<DT 12>
*

*> Created a new atom named: H2' within residue: .R<DT 12>
*

*> Created a new atom named: H2'' within residue: .R<DT 12>
*

*> Created a new atom named: H5' within residue: .R<DG 13>
*

*> Created a new atom named: H5'' within residue: .R<DG 13>
*

*> Created a new atom named: H2' within residue: .R<DG 13>
*

*> Created a new atom named: H2'' within residue: .R<DG 13>
*

*> Created a new atom named: H5' within residue: .R<DT 14>
*

*> Created a new atom named: H5'' within residue: .R<DT 14>
*

*> Created a new atom named: H2' within residue: .R<DT 14>
*

*> Created a new atom named: H2'' within residue: .R<DT 14>
*

*> Created a new atom named: H5' within residue: .R<DT 15>
*

*> Created a new atom named: H5'' within residue: .R<DT 15>
*

*> Created a new atom named: H2' within residue: .R<DT 15>
*

*> Created a new atom named: H2'' within residue: .R<DT 15>
*

*> Created a new atom named: H5' within residue: .R<DT 16>
*

*> Created a new atom named: H5'' within residue: .R<DT 16>
*

*> Created a new atom named: H2' within residue: .R<DT 16>
*

*> Created a new atom named: H2'' within residue: .R<DT 16>
*

*> Created a new atom named: H5' within residue: .R<DA 17>
*

*> Created a new atom named: H5'' within residue: .R<DA 17>
*

*> Created a new atom named: H2' within residue: .R<DA 17>
*

*> Created a new atom named: H2'' within residue: .R<DA 17>
*

*> Created a new atom named: H5' within residue: .R<DT 18>
*

*> Created a new atom named: H5'' within residue: .R<DT 18>
*

*> Created a new atom named: H2' within residue: .R<DT 18>
*

*> Created a new atom named: H2'' within residue: .R<DT 18>
*

*> Created a new atom named: HO3' within residue: .R<DT 18>
*

*> Created a new atom named: HO5' within residue: .R<DA 19>
*

*> Created a new atom named: H5' within residue: .R<DA 19>
*

*> Created a new atom named: H5'' within residue: .R<DA 19>
*

*> Created a new atom named: H2' within residue: .R<DA 19>
*

*> Created a new atom named: H2'' within residue: .R<DA 19>
*

*> Added missing heavy atom: .R<DA 19>.A<P 1>
*

*> Added missing heavy atom: .R<DA 19>.A<O1P 2>
*

*> Added missing heavy atom: .R<DA 19>.A<O2P 3>
*

*> Created a new atom named: H5' within residue: .R<DT 20>
*

*> Created a new atom named: H5'' within residue: .R<DT 20>
*

*> Created a new atom named: H2' within residue: .R<DT 20>
*

*> Created a new atom named: H2'' within residue: .R<DT 20>
*

*> Created a new atom named: H5' within residue: .R<DA 21>
*

*> Created a new atom named: H5'' within residue: .R<DA 21>
*

*> Created a new atom named: H2' within residue: .R<DA 21>
*

*> Created a new atom named: H2'' within residue: .R<DA 21>
*

*> Created a new atom named: H5' within residue: .R<DA 22>
*

*> Created a new atom named: H5'' within residue: .R<DA 22>
*

*> Created a new atom named: H2' within residue: .R<DA 22>
*

*> Created a new atom named: H2'' within residue: .R<DA 22>
*

*> Created a new atom named: H5' within residue: .R<DA 23>
*

*> Created a new atom named: H5'' within residue: .R<DA 23>
*

*> Created a new atom named: H2' within residue: .R<DA 23>
*

*> Created a new atom named: H2'' within residue: .R<DA 23>
*

*> Created a new atom named: H5' within residue: .R<DC 24>
*

*> Created a new atom named: H5'' within residue: .R<DC 24>
*

*> Created a new atom named: H2' within residue: .R<DC 24>
*

*> Created a new atom named: H2'' within residue: .R<DC 24>
*

*> Created a new atom named: H5' within residue: .R<DA 25>
*

*> Created a new atom named: H5'' within residue: .R<DA 25>
*

*> Created a new atom named: H2' within residue: .R<DA 25>
*

*> Created a new atom named: H2'' within residue: .R<DA 25>
*

*> Created a new atom named: H5' within residue: .R<DG 26>
*

*> Created a new atom named: H5'' within residue: .R<DG 26>
*

*> Created a new atom named: H2' within residue: .R<DG 26>
*

*> Created a new atom named: H2'' within residue: .R<DG 26>
*

*> Created a new atom named: H5' within residue: .R<DT 27>
*

*> Created a new atom named: H5'' within residue: .R<DT 27>
*

*> Created a new atom named: H2' within residue: .R<DT 27>
*

*> Created a new atom named: H2'' within residue: .R<DT 27>
*

*> Created a new atom named: H5' within residue: .R<DT 28>
*

*> Created a new atom named: H5'' within residue: .R<DT 28>
*

*> Created a new atom named: H2' within residue: .R<DT 28>
*

*> Created a new atom named: H2'' within residue: .R<DT 28>
*

*> Created a new atom named: H5' within residue: .R<DA 29>
*

*> Created a new atom named: H5'' within residue: .R<DA 29>
*

*> Created a new atom named: H2' within residue: .R<DA 29>
*

*> Created a new atom named: H2'' within residue: .R<DA 29>
*

*> Created a new atom named: H5' within residue: .R<DA 30>
*

*> Created a new atom named: H5'' within residue: .R<DA 30>
*

*> Created a new atom named: H2' within residue: .R<DA 30>
*

*> Created a new atom named: H2'' within residue: .R<DA 30>
*

*> Created a new atom named: H5' within residue: .R<DT 31>
*

*> Created a new atom named: H5'' within residue: .R<DT 31>
*

*> Created a new atom named: H2' within residue: .R<DT 31>
*

*> Created a new atom named: H2'' within residue: .R<DT 31>
*

*> Created a new atom named: H5' within residue: .R<DA 32>
*

*> Created a new atom named: H5'' within residue: .R<DA 32>
*

*> Created a new atom named: H2' within residue: .R<DA 32>
*

*> Created a new atom named: H2'' within residue: .R<DA 32>
*

*> Created a new atom named: H5' within residue: .R<DA 33>
*

*> Created a new atom named: H5'' within residue: .R<DA 33>
*

*> Created a new atom named: H2' within residue: .R<DA 33>
*

*> Created a new atom named: H2'' within residue: .R<DA 33>
*

*> Created a new atom named: H5' within residue: .R<DA 34>
*

*> Created a new atom named: H5'' within residue: .R<DA 34>
*

*> Created a new atom named: H2' within residue: .R<DA 34>
*

*> Created a new atom named: H2'' within residue: .R<DA 34>
*

*> Created a new atom named: H5' within residue: .R<DC 35>
*

*> Created a new atom named: H5'' within residue: .R<DC 35>
*

*> Created a new atom named: H2' within residue: .R<DC 35>
*

*> Created a new atom named: H2'' within residue: .R<DC 35>
*

*> Created a new atom named: H5' within residue: .R<DC 36>
*

*> Created a new atom named: H5'' within residue: .R<DC 36>
*

*> Created a new atom named: H2' within residue: .R<DC 36>
*

*> Created a new atom named: H2'' within residue: .R<DC 36>
*

*> Created a new atom named: HO3' within residue: .R<DC 36>
*

*> total atoms in file: 1146
*

*> Leap added 150 missing atoms according to residue templates:
*

*> 6 Heavy
*

*> 144 H / lone pairs
*

*> The file contained 148 atoms not in residue templates
*

*>
*

*> then i tried to save parametersas follows:
*

*>
*

*> > saveamberparm dna1 dna1.prmtop dna1.inpcrd
*

*> Checking Unit.
*

*> WARNING: There is a bond of 12.226016 angstroms between:
*

*> ------- .R<DG 1>.A<O3' 33> and .R<DG 2>.A<P 1>
*

*> WARNING: There is a bond of 6.335369 angstroms between:
*

*> ------- .R<DG 1>.A<C3' 28> and .R<DG 1>.A<H3' 29>
*

*> WARNING: There is a bond of 8.285898 angstroms between:
*

*> ------- .R<DG 1>.A<C3' 28> and .R<DG 1>.A<C2' 30>
*

*> WARNING: There is a bond of 4.677275 angstroms between:
*

*> ------- .R<DG 1>.A<C3' 28> and .R<DG 1>.A<O3' 33>
*

*> WARNING: There is a bond of 4.385442 angstroms between:
*

*> ------- .R<DG 1>.A<N3 26> and .R<DG 1>.A<C4 27>
*

*> WARNING: There is a bond of 8.603162 angstroms between:
*

*> ------- .R<DG 1>.A<N2 23> and .R<DG 1>.A<H21 24>
*

*> WARNING: There is a bond of 10.044083 angstroms between:
*

*> ------- .R<DG 1>.A<N2 23> and .R<DG 1>.A<H22 25>
*

*> WARNING: There is a bond of 5.093221 angstroms between:
*

*> ------- .R<DG 1>.A<C2 22> and .R<DG 1>.A<N2 23>
*

*> WARNING: There is a bond of 5.008403 angstroms between:
*

*> ------- .R<DG 1>.A<C2 22> and .R<DG 1>.A<N3 26>
*

*> WARNING: There is a bond of 7.725930 angstroms between:
*

*> ------- .R<DG 1>.A<N1 20> and .R<DG 1>.A<C2 22>
*

*> WARNING: There is a bond of 6.797794 angstroms between:
*

*> ------- .R<DG 1>.A<C6 18> and .R<DG 1>.A<O6 19>
*

*> WARNING: There is a bond of 8.562856 angstroms between:
*

*> ------- .R<DG 1>.A<C6 18> and .R<DG 1>.A<N1 20>
*

*> WARNING: There is a bond of 6.091174 angstroms between:
*

*> ------- .R<DG 1>.A<C5 17> and .R<DG 1>.A<C6 18>
*

*> WARNING: There is a bond of 7.191391 angstroms between:
*

*> ------- .R<DG 1>.A<C5 17> and .R<DG 1>.A<C4 27>
*

*> WARNING: There is a bond of 7.076221 angstroms between:
*

*> ------- .R<DG 1>.A<C8 14> and .R<DG 1>.A<H8 15>
*

*> WARNING: There is a bond of 7.659791 angstroms between:
*

*> ------- .R<DG 1>.A<C8 14> and .R<DG 1>.A<N7 16>
*

*> WARNING: There is a bond of 6.224339 angstroms between:
*

*> ------- .R<DG 1>.A<N9 13> and .R<DG 1>.A<C8 14>
*

*> WARNING: There is a bond of 8.062264 angstroms between:
*

*> ------- .R<DG 1>.A<N9 13> and .R<DG 1>.A<C4 27>
*

*> WARNING: There is a bond of 6.756930 angstroms between:
*

*> ------- .R<DG 1>.A<C1' 11> and .R<DG 1>.A<H1' 12>
*

*> WARNING: There is a bond of 5.144327 angstroms between:
*

*> ------- .R<DG 1>.A<C1' 11> and .R<DG 1>.A<N9 13>
*

*> WARNING: There is a bond of 6.002133 angstroms between:
*

*> ------- .R<DG 1>.A<C1' 11> and .R<DG 1>.A<C2' 30>
*

*> WARNING: There is a bond of 3.166844 angstroms between:
*

*> ------- .R<DG 1>.A<O4' 10> and .R<DG 1>.A<C1' 11>
*

*> WARNING: There is a bond of 6.146088 angstroms between:
*

*> ------- .R<DG 1>.A<C4' 8> and .R<DG 1>.A<H4' 9>
*

*> WARNING: There is a bond of 8.606254 angstroms between:
*

*> ------- .R<DG 1>.A<C4' 8> and .R<DG 1>.A<C3' 28>
*

*> WARNING: There is a bond of 7.282884 angstroms between:
*

*> ------- .R<DG 1>.A<O5' 4> and .R<DG 1>.A<C5' 5>
*

*> WARNING: There is a bond of 53.957076 angstroms between:
*

*> ------- .R<DA 17>.A<O3' 32> and .R<DT 18>.A<P 1>
*

*> WARNING: There is a bond of 4.156549 angstroms between:
*

*> ------- .R<DT 18>.A<C3' 27> and .R<DT 18>.A<C2' 29>
*

*> WARNING: There is a bond of 5.668942 angstroms between:
*

*> ------- .R<DT 18>.A<C3' 27> and .R<DT 18>.A<O3' 32>
*

*> WARNING: There is a bond of 4.125155 angstroms between:
*

*> ------- .R<DT 18>.A<C2 25> and .R<DT 18>.A<O2 26>
*

*> WARNING: There is a bond of 6.779410 angstroms between:
*

*> ------- .R<DT 18>.A<N3 23> and .R<DT 18>.A<H3 24>
*

*> WARNING: There is a bond of 6.495237 angstroms between:
*

*> ------- .R<DT 18>.A<N3 23> and .R<DT 18>.A<C2 25>
*

*> WARNING: There is a bond of 6.409493 angstroms between:
*

*> ------- .R<DT 18>.A<C4 21> and .R<DT 18>.A<O4 22>
*

*> WARNING: There is a bond of 7.140035 angstroms between:
*

*> ------- .R<DT 18>.A<C7 17> and .R<DT 18>.A<H72 19>
*

*> WARNING: There is a bond of 5.405636 angstroms between:
*

*> ------- .R<DT 18>.A<C7 17> and .R<DT 18>.A<H73 20>
*

*> WARNING: There is a bond of 4.125155 angstroms between:
*

*> ------- .R<DT 18>.A<C5 16> and .R<DT 18>.A<C7 17>
*

*> WARNING: There is a bond of 10.676146 angstroms between:
*

*> ------- .R<DT 18>.A<C6 14> and .R<DT 18>.A<H6 15>
*

*> WARNING: There is a bond of 5.113208 angstroms between:
*

*> ------- .R<DT 18>.A<C6 14> and .R<DT 18>.A<C5 16>
*

*> WARNING: There is a bond of 6.084152 angstroms between:
*

*> ------- .R<DT 18>.A<N1 13> and .R<DT 18>.A<C6 14>
*

*> WARNING: There is a bond of 5.521630 angstroms between:
*

*> ------- .R<DT 18>.A<N1 13> and .R<DT 18>.A<C2 25>
*

*> WARNING: There is a bond of 6.413236 angstroms between:
*

*> ------- .R<DT 18>.A<C1' 11> and .R<DT 18>.A<H1' 12>
*

*> WARNING: There is a bond of 4.294182 angstroms between:
*

*> ------- .R<DT 18>.A<C1' 11> and .R<DT 18>.A<N1 13>
*

*> WARNING: There is a bond of 6.205876 angstroms between:
*

*> ------- .R<DT 18>.A<C1' 11> and .R<DT 18>.A<C2' 29>
*

*> WARNING: There is a bond of 5.110342 angstroms between:
*

*> ------- .R<DT 18>.A<O4' 10> and .R<DT 18>.A<C1' 11>
*

*> WARNING: There is a bond of 6.410624 angstroms between:
*

*> ------- .R<DT 18>.A<C4' 8> and .R<DT 18>.A<H4' 9>
*

*> WARNING: There is a bond of 9.322253 angstroms between:
*

*> ------- .R<DT 18>.A<C4' 8> and .R<DT 18>.A<O4' 10>
*

*> WARNING: There is a bond of 3.226391 angstroms between:
*

*> ------- .R<DT 18>.A<C4' 8> and .R<DT 18>.A<C3' 27>
*

*> WARNING: There is a bond of 4.123882 angstroms between:
*

*> ------- .R<DT 18>.A<C5' 5> and .R<DT 18>.A<C4' 8>
*

*> WARNING: There is a bond of 5.830960 angstroms between:
*

*> ------- .R<DT 18>.A<O5' 4> and .R<DT 18>.A<C5' 5>
*

*> WARNING: There is a bond of 9.547822 angstroms between:
*

*> ------- .R<DT 18>.A<P 1> and .R<DT 18>.A<O1P 2>
*

*> WARNING: There is a bond of 4.284857 angstroms between:
*

*> ------- .R<DT 18>.A<P 1> and .R<DT 18>.A<O2P 3>
*

*> WARNING: There is a bond of 4.304985 angstroms between:
*

*> ------- .R<DT 18>.A<P 1> and .R<DT 18>.A<O5' 4>
*

*> WARNING: There is a bond of 54.574569 angstroms between:
*

*> ------- .R<DA 19>.A<O3' 32> and .R<DT 20>.A<P 1>
*

*> WARNING: There is a bond of 4.143235 angstroms between:
*

*> ------- .R<DA 19>.A<C3' 27> and .R<DA 19>.A<H3' 28>
*

*> WARNING: There is a bond of 5.040794 angstroms between:
*

*> ------- .R<DA 19>.A<C3' 27> and .R<DA 19>.A<C2' 29>
*

*> WARNING: There is a bond of 6.726076 angstroms between:
*

*> ------- .R<DA 19>.A<C3' 27> and .R<DA 19>.A<O3' 32>
*

*> WARNING: There is a bond of 6.797794 angstroms between:
*

*> ------- .R<DA 19>.A<N3 25> and .R<DA 19>.A<C4 26>
*

*> WARNING: There is a bond of 6.796183 angstroms between:
*

*> ------- .R<DA 19>.A<C2 23> and .R<DA 19>.A<N3 25>
*

*> WARNING: There is a bond of 5.001210 angstroms between:
*

*> ------- .R<DA 19>.A<N1 22> and .R<DA 19>.A<C2 23>
*

*> WARNING: There is a bond of 5.166130 angstroms between:
*

*> ------- .R<DA 19>.A<N6 19> and .R<DA 19>.A<H62 21>
*

*> WARNING: There is a bond of 8.602906 angstroms between:
*

*> ------- .R<DA 19>.A<C6 18> and .R<DA 19>.A<N6 19>
*

*> WARNING: There is a bond of 7.296033 angstroms between:
*

*> ------- .R<DA 19>.A<C6 18> and .R<DA 19>.A<N1 22>
*

*> WARNING: There is a bond of 3.393066 angstroms between:
*

*> ------- .R<DA 19>.A<C5 17> and .R<DA 19>.A<C6 18>
*

*> WARNING: There is a bond of 5.000160 angstroms between:
*

*> ------- .R<DA 19>.A<C5 17> and .R<DA 19>.A<C4 26>
*

*> WARNING: There is a bond of 3.422879 angstroms between:
*

*> ------- .R<DA 19>.A<N7 16> and .R<DA 19>.A<C5 17>
*

*> WARNING: There is a bond of 3.027606 angstroms between:
*

*> ------- .R<DA 19>.A<C8 14> and .R<DA 19>.A<H8 15>
*

*> WARNING: There is a bond of 5.153882 angstroms between:
*

*> ------- .R<DA 19>.A<N9 13> and .R<DA 19>.A<C8 14>
*

*> WARNING: There is a bond of 3.419064 angstroms between:
*

*> ------- .R<DA 19>.A<N9 13> and .R<DA 19>.A<C4 26>
*

*> WARNING: There is a bond of 4.207802 angstroms between:
*

*> ------- .R<DA 19>.A<C1' 11> and .R<DA 19>.A<H1' 12>
*

*> WARNING: There is a bond of 9.230038 angstroms between:
*

*> ------- .R<DA 19>.A<C1' 11> and .R<DA 19>.A<N9 13>
*

*> WARNING: There is a bond of 4.332309 angstroms between:
*

*> ------- .R<DA 19>.A<C1' 11> and .R<DA 19>.A<C2' 29>
*

*> WARNING: There is a bond of 3.008804 angstroms between:
*

*> ------- .R<DA 19>.A<O4' 10> and .R<DA 19>.A<C1' 11>
*

*> WARNING: There is a bond of 7.619554 angstroms between:
*

*> ------- .R<DA 19>.A<C4' 8> and .R<DA 19>.A<H4' 9>
*

*> WARNING: There is a bond of 7.320355 angstroms between:
*

*> ------- .R<DA 19>.A<C4' 8> and .R<DA 19>.A<O4' 10>
*

*> WARNING: There is a bond of 5.022987 angstroms between:
*

*> ------- .R<DA 19>.A<C4' 8> and .R<DA 19>.A<C3' 27>
*

*> WARNING: There is a bond of 3.274523 angstroms between:
*

*> ------- .R<DA 19>.A<C5' 5> and .R<DA 19>.A<C4' 8>
*

*> WARNING: There is a bond of 4.169460 angstroms between:
*

*> ------- .R<DA 19>.A<O5' 4> and .R<DA 19>.A<C5' 5>
*

*> WARNING: There is a bond of 5.569182 angstroms between:
*

*> ------- .R<DC 35>.A<O3' 30> and .R<DC 36>.A<P 1>
*

*> WARNING: There is a bond of 6.335369 angstroms between:
*

*> ------- .R<DC 36>.A<C3' 25> and .R<DC 36>.A<H3' 26>
*

*> WARNING: There is a bond of 8.285898 angstroms between:
*

*> ------- .R<DC 36>.A<C3' 25> and .R<DC 36>.A<C2' 27>
*

*> WARNING: There is a bond of 4.677275 angstroms between:
*

*> ------- .R<DC 36>.A<C3' 25> and .R<DC 36>.A<O3' 30>
*

*> WARNING: There is a bond of 4.620130 angstroms between:
*

*> ------- .R<DC 36>.A<C2 23> and .R<DC 36>.A<O2 24>
*

*> WARNING: There is a bond of 4.145853 angstroms between:
*

*> ------- .R<DC 36>.A<N3 22> and .R<DC 36>.A<C2 23>
*

*> WARNING: There is a bond of 6.327409 angstroms between:
*

*> ------- .R<DC 36>.A<N4 19> and .R<DC 36>.A<H41 20>
*

*> WARNING: There is a bond of 6.156501 angstroms between:
*

*> ------- .R<DC 36>.A<N4 19> and .R<DC 36>.A<H42 21>
*

*> WARNING: There is a bond of 4.635558 angstroms between:
*

*> ------- .R<DC 36>.A<C4 18> and .R<DC 36>.A<N3 22>
*

*> WARNING: There is a bond of 3.738997 angstroms between:
*

*> ------- .R<DC 36>.A<C5 16> and .R<DC 36>.A<H5 17>
*

*> WARNING: There is a bond of 5.100431 angstroms between:
*

*> ------- .R<DC 36>.A<C6 14> and .R<DC 36>.A<H6 15>
*

*> WARNING: There is a bond of 3.769615 angstroms between:
*

*> ------- .R<DC 36>.A<C6 14> and .R<DC 36>.A<C5 16>
*

*> WARNING: There is a bond of 7.716061 angstroms between:
*

*> ------- .R<DC 36>.A<N1 13> and .R<DC 36>.A<C6 14>
*

*> WARNING: There is a bond of 5.102558 angstroms between:
*

*> ------- .R<DC 36>.A<N1 13> and .R<DC 36>.A<C2 23>
*

*> WARNING: There is a bond of 6.376214 angstroms between:
*

*> ------- .R<DC 36>.A<C1' 11> and .R<DC 36>.A<H1' 12>
*

*> WARNING: There is a bond of 5.144327 angstroms between:
*

*> ------- .R<DC 36>.A<C1' 11> and .R<DC 36>.A<N1 13>
*

*> WARNING: There is a bond of 6.002133 angstroms between:
*

*> ------- .R<DC 36>.A<C1' 11> and .R<DC 36>.A<C2' 27>
*

*> WARNING: There is a bond of 3.166844 angstroms between:
*

*> ------- .R<DC 36>.A<O4' 10> and .R<DC 36>.A<C1' 11>
*

*> WARNING: There is a bond of 6.146088 angstroms between:
*

*> ------- .R<DC 36>.A<C4' 8> and .R<DC 36>.A<H4' 9>
*

*> WARNING: There is a bond of 8.606254 angstroms between:
*

*> ------- .R<DC 36>.A<C4' 8> and .R<DC 36>.A<C3' 25>
*

*> WARNING: There is a bond of 7.282884 angstroms between:
*

*> ------- .R<DC 36>.A<O5' 4> and .R<DC 36>.A<C5' 5>
*

*> WARNING: There is a bond of 9.917661 angstroms between:
*

*> ------- .R<DC 36>.A<P 1> and .R<DC 36>.A<O1P 2>
*

*> WARNING: There is a bond of 5.961342 angstroms between:
*

*> ------- .R<DC 36>.A<P 1> and .R<DC 36>.A<O2P 3>
*

*> WARNING: There is a bond of 3.185106 angstroms between:
*

*> ------- .R<DC 36>.A<P 1> and .R<DC 36>.A<O5' 4>
*

*> WARNING: The unperturbed charge of the unit: -36.000000 is not zero.
*

*> FATAL: Atom .R<DG 1>.A<HO5' 34> does not have a type.
*

*> FATAL: Atom .R<DG 1>.A<H5' 35> does not have a type.
*

*> FATAL: Atom .R<DG 1>.A<H5'' 36> does not have a type.
*

*> FATAL: Atom .R<DG 1>.A<H2' 37> does not have a type.
*

*> FATAL: Atom .R<DG 1>.A<H2'' 38> does not have a type.
*

*> FATAL: Atom .R<DG 2>.A<H5' 34> does not have a type.
*

*> FATAL: Atom .R<DG 2>.A<H5'' 35> does not have a type.
*

*> FATAL: Atom .R<DG 2>.A<H2' 36> does not have a type.
*

*> FATAL: Atom .R<DG 2>.A<H2'' 37> does not have a type.
*

*> FATAL: Atom .R<DT 3>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DT 3>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DT 3>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DT 3>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DT 4>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DT 4>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DT 4>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DT 4>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DT 5>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DT 5>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DT 5>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DT 5>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DA 6>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DA 6>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DA 6>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DA 6>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DT 7>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DT 7>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DT 7>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DT 7>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DT 8>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DT 8>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DT 8>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DT 8>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DA 9>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DA 9>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DA 9>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DA 9>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DA 10>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DA 10>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DA 10>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DA 10>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DC 11>.A<H5' 31> does not have a type.
*

*> FATAL: Atom .R<DC 11>.A<H5'' 32> does not have a type.
*

*> FATAL: Atom .R<DC 11>.A<H2' 33> does not have a type.
*

*> FATAL: Atom .R<DC 11>.A<H2'' 34> does not have a type.
*

*> FATAL: Atom .R<DT 12>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DT 12>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DT 12>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DT 12>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DG 13>.A<H5' 34> does not have a type.
*

*> FATAL: Atom .R<DG 13>.A<H5'' 35> does not have a type.
*

*> FATAL: Atom .R<DG 13>.A<H2' 36> does not have a type.
*

*> FATAL: Atom .R<DG 13>.A<H2'' 37> does not have a type.
*

*> FATAL: Atom .R<DT 14>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DT 14>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DT 14>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DT 14>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DT 15>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DT 15>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DT 15>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DT 15>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DT 16>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DT 16>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DT 16>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DT 16>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DA 17>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DA 17>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DA 17>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DA 17>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DT 18>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DT 18>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DT 18>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DT 18>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DT 18>.A<HO3' 37> does not have a type.
*

*> FATAL: Atom .R<DA 19>.A<HO5' 33> does not have a type.
*

*> FATAL: Atom .R<DA 19>.A<H5' 34> does not have a type.
*

*> FATAL: Atom .R<DA 19>.A<H5'' 35> does not have a type.
*

*> FATAL: Atom .R<DA 19>.A<H2' 36> does not have a type.
*

*> FATAL: Atom .R<DA 19>.A<H2'' 37> does not have a type.
*

*> FATAL: Atom .R<DT 20>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DT 20>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DT 20>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DT 20>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DA 21>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DA 21>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DA 21>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DA 21>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DA 22>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DA 22>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DA 22>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DA 22>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DA 23>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DA 23>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DA 23>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DA 23>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DC 24>.A<H5' 31> does not have a type.
*

*> FATAL: Atom .R<DC 24>.A<H5'' 32> does not have a type.
*

*> FATAL: Atom .R<DC 24>.A<H2' 33> does not have a type.
*

*> FATAL: Atom .R<DC 24>.A<H2'' 34> does not have a type.
*

*> FATAL: Atom .R<DA 25>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DA 25>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DA 25>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DA 25>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DG 26>.A<H5' 34> does not have a type.
*

*> FATAL: Atom .R<DG 26>.A<H5'' 35> does not have a type.
*

*> FATAL: Atom .R<DG 26>.A<H2' 36> does not have a type.
*

*> FATAL: Atom .R<DG 26>.A<H2'' 37> does not have a type.
*

*> FATAL: Atom .R<DT 27>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DT 27>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DT 27>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DT 27>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DT 28>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DT 28>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DT 28>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DT 28>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DA 29>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DA 29>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DA 29>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DA 29>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DA 30>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DA 30>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DA 30>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DA 30>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DT 31>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DT 31>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DT 31>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DT 31>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DA 32>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DA 32>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DA 32>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DA 32>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DA 33>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DA 33>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DA 33>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DA 33>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DA 34>.A<H5' 33> does not have a type.
*

*> FATAL: Atom .R<DA 34>.A<H5'' 34> does not have a type.
*

*> FATAL: Atom .R<DA 34>.A<H2' 35> does not have a type.
*

*> FATAL: Atom .R<DA 34>.A<H2'' 36> does not have a type.
*

*> FATAL: Atom .R<DC 35>.A<H5' 31> does not have a type.
*

*> FATAL: Atom .R<DC 35>.A<H5'' 32> does not have a type.
*

*> FATAL: Atom .R<DC 35>.A<H2' 33> does not have a type.
*

*> FATAL: Atom .R<DC 35>.A<H2'' 34> does not have a type.
*

*> FATAL: Atom .R<DC 36>.A<H5' 31> does not have a type.
*

*> FATAL: Atom .R<DC 36>.A<H5'' 32> does not have a type.
*

*> FATAL: Atom .R<DC 36>.A<H2' 33> does not have a type.
*

*> FATAL: Atom .R<DC 36>.A<H2'' 34> does not have a type.
*

*> FATAL: Atom .R<DC 36>.A<HO3' 35> does not have a type.
*

*> Failed to generate parameters
*

*> Parameter file was not saved.
*

*>
*

*> now why atomtype is not being defined .this is the main problem.
*

*> i'l be very thankful for your kind help
*

*>
*

*> thanx
*

*> monica
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*> > On Fri, Jun 25, 2010, monica.imtech.res.in wrote:
*

*> >
*

*> >> actually i also got HO5' only but seeing some tutorial referance i
*

*> changed to
*

*> >> H5T.
*

*> >
*

*> > What happens if you don't make such changes, and continue to use
*

*> AmberTools
*

*> > 1.4?
*

*> >
*

*> >> and did u see that the terminal residues are not correctly bonded.
*

*> >
*

*> > Can you say exactly what is "not correctly bonded", and why you came to
*

*> that
*

*> > conclusion?
*

*> >
*

*> >> still i am facing same problem of not getting parameters
*

*> >
*

*> > We need *specific* problem reports: the actual inputs, and exact error
*

*> > messages. Try to see how what you are doing is different from that shown
*

*> > in Tutorial B1.
*

*> >
*

*> > ....dac
*

*> >
*

*> >
*

*> > _______________________________________________
*

*> > AMBER mailing list
*

*> > AMBER.ambermd.org
*

*> > http://lists.ambermd.org/mailman/listinfo/amber
*

*> >
*

*> >
*

*>
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

Date: Sun, 27 Jun 2010 12:56:03 -0400

Hi, Monica,

Once you built the DNA with NAB, did you load the output PDB into

visualization program, like Chimera, or VMD, and then re-save the PDB before

loading it into leap?

It's weird that only the hydrogen atom names are the problem. Usually,

visualization programs like Chimera, or VMD, etc., have their own hydrogen

atom naming conventions, which are usually NOT acceptable by AMBER (leap,

that is).

-kevin

On Sun, Jun 27, 2010 at 12:50 AM, <monica.imtech.res.in> wrote:

-- -- - - HK ------------------------------------------------------- Kevin Eduard Hauser National Science Foundation, LSAMP Bridge to the Doctorate Fellow The Department of Chemistry Stony Brook University Stony Brook, New York 11794 Phone: (561) 635.1848 Email: 84hauser.gmail.com ------------------------------------------------------- _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sun Jun 27 2010 - 10:00:03 PDT

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