[gmx-users] DNA with charmm27 works fine but why

gromacs query gromacsquery at gmail.com
Tue Feb 4 17:50:33 CET 2014

Hi All

I have built DNA with NAB in AMBER and it provide names as D*, D*3, D*5
(where * = A,T,G,C) and want to use charmm27 in gromacs. The
charmm27.ff/dna.rtp does not have D*5 or D*3 and has only D* residues, so I
renamed D*5 or D*3 to just corresponding D* residues. The output pdb with
pdb2gmx as looked in vmd is fine but why?
As far as I know in gromacs the sequence of loading structure should match
rtp file. So I have following two queries:

1) Here is comparison for DA residue (non-terminal):

#My   #charmm27/dna.rtp

 P     P
 OP1   O1P <still ok as gromacs will rename atom; No problem
 OP2   O2P <still ok as gromacs will rename atom
 O5'   O5'
 C5'   C5'
 H5'   H5'1 <still ok as gromacs will rename atom
 H5''  H5'2  <still ok as gromacs will rename atom
 C4'   C4'
 H4'   H4'
 O4'   O4'
 C1'   C1'
 H1'   H1'
 N9    N9
 C8    C5  < difference starts
 H8    N7
 N7    C8
 C5    H8
 C6    N1
 N6    C2
 H61   H2
 H62   N3
 N1    C4
 C2    C6
 H2    N6
 N3    H61
 C4    H62
 C3'   C2'
 H3'   H2'1
 C2'   H2'2
 H2'   C3'
 H2''  H3'
 O3'   O3'

2) Also I noticed as there are no D*3 or D*5 exist in dna.rtp, somehow
gromacs add/deletes atoms from dna.c.tdb or dna.n.tdb files and finally I
get correct atoms. But same here also atom sequence is not same!

best regards

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