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

[gromacs query]

Hi Justin

>> Presence of the correct atoms is the only absolute requirement

Thanks. Correct 'atoms' mean correct 'atom names'? so does that mean I
should rename my atoms according to rtp file?

Also one more question: I think atom order does matter when I load a pdb
and use some .top file? (and if I understood it correctly; if I am using
from rtp file, which is a sort of residue library file, then order does NOT
matter)

thanks


On Tue, Feb 4, 2014 at 5:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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