Re: [gmx-users] DNA topology error

[Justin Lemkul]

On 7/11/17 3:40 PM, maria khan wrote:

dear Mark Abraham

According to my error like  """Residue 9 named DG of a molecule in the
input file was mapped to an entry in the topology database, but the atom
O5' used in that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed."""

if O5' can be set in pdb manually,then how  the other values of
cordinates   (figures) can be provided manually,as these values are
experimental.



Regular B-form DNA has a predictable structure.  If yours is incomplete, there 
are a variety of utilities that you can use to model in the missing atoms.  Just 
Google around.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] DNA topology error

[maria khan]

dear Mark Abraham

According to my error like  """Residue 9 named DG of a molecule in the
input file was mapped to an entry in the topology database, but the atom
O5' used in that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed."""

if O5' can be set in pdb manually,then how  the other values of
cordinates   (figures) can be provided manually,as these values are
experimental.

Thanks.

Maria.
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Re: [gmx-users] DNa topology error.

[Mark Abraham]

Hi,

pdb2gmx found a residue called DG and found an rtp entry that matched it.
It just didn't find an O5' atom within it. You should also be able to find
that residue.

Mark

On Tue, Jul 11, 2017 at 5:26 PM maria khan 
wrote:

> Thanks Mark Abraham.
>
> i would like to share my pdb file as still i dont understand the error as
> well as your answer,kindly look at this then explain it.
> it cant be shared as the file is large.i checked the file in front of
> residue 9,there is no DG at all .All along the chains is DA.
> regards.
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[gmx-users] DNa topology error.

[maria khan]

Thanks Mark Abraham.

i would like to share my pdb file as still i dont understand the error as
well as your answer,kindly look at this then explain it.
it cant be shared as the file is large.i checked the file in front of
residue 9,there is no DG at all .All along the chains is DA.
regards.
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