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

Justin Lemkul jalemkul at vt.edu
Tue Feb 4 18:05:28 CET 2014

On 2/4/14, 11:50 AM, gromacs query wrote:
> 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?

When dealing with terminal nucleotides, pdb2gmx understands 5' and 3' without 
having digits as part of residue names.

> 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!

Order of atoms is irrelevant.  Presence of the correct atoms is the only 
absolute requirement.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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