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A question of building dsDNA
#808 01/06/04 08:51 AM
Joined: Dec 2003
Posts: 80
L
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Hello everybody..
I try the gen-dna.inp from "Lennart Nilsson, Karolinska Institutet".And I use InsightII to build atcg.pdb for the script .
When I run the script , the error message is above .Someone
can tell me how to fix the problem . Thanks.
yeng-tseng


-------------------------------------------------------------------------
VOPEN> Attempting to open::/home/c00jsw00/atcg.pdb::
SPATIAL COORDINATES BEING READ FROM UNIT 90
TITLE> *

** WARNING ** For atom in coordinate file, could not find residue in PSF, and i
thus ignored:

SEGID=DNA1 RESID=1 RESNAME= A TYPE= P
*** LEVEL 1 WARNING *** BOMLEV IS 0

Re: A question of building dsDNA
label #809 01/06/04 10:26 AM
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Insight and CHARMM used different names for the nucleotides; the error message indicates that there is a residue named "A" in the Insight pdb file, but CHARMM expects the name ADE, as is also clear from gen-dna.inp.
If you used gen-dna.inp exactly as posted there are also other inconsistencies in your atcg.pdb file. The segids should be A and B (not DNA1) and there should be no 5' or 3' phosphate groups in the structure
! No end phosphate groups
gene a first 5ter last 3ter

There is a tar-file containing my examples, and the pdb files they use, at:
www.biosci.ki.se/md/charmm.html


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  lennart, rmv 

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