[gmx-users] topology for large molecule

[Daan van Aalten]

Hi Hideki

Simulating NAG6 on a chitinase or chitin binding protein is indeed a
problem. The problem lies certainly not in GMX, but in PRODRG which for
historic reasons can currently only do 100 total atoms (i.e. your 85 + 6 *
~6 hydrogens = > 100). This will be corrected before 1-1-2002.
In that case no need to worry about the linkages as they would be taken
care of automatically.

I think GROMOS used to have a NAG residue in the building block file, so
perhaps the GMX people could comment on how that can be translated to GMX?
Alternatively, you could make a NAG topology with PRODRG and then define
additional bonds to make the beta(1,4) linkages.

cheers

Daan


On Thu, 15 Nov 2001, Hideki Takehara wrote:

> Hello everyone,
> 
>     I want to do MD simulation of a protein including sugar polymers.  I
> believe the gromacs is very sophisticate system to do so. but  I am a
> beginner for using gromacs, so please anybody help me. my questions are
> 1. How to create topology of large molecules. At first, I was attempt to
> do with PRODRG server, but it said my molecule is too large to create
> topology. My molecule is hexa-GlcNAc(N-acetyl glucosamin) which has 85
> atoms without hydrogen. PRODRG said it is impossible because of
> limitation of gromacs topolgy discription.
> 2. How to define connectivity between monomers. Next, I tried to create
> a topolgy file for monomer and
> connect them like amino acid chain. But I can not find files or data
> about this. I guess I can add GlcNAc to aminoacid.dat file like the case
> of a modified  amino acid. but I am wondering how to treate gycosil
> bonds.
>     I guess this might be FAQ??
>     Please give me your help. Thanks in advance.
> 
> 
> --
> Hideki Takehara  take at grt.kyushu-u.ac.jp
> Molecular Gene Technics, Genetic Resource Technology,
>           Kyushu University
>               Tel +81-92-642-3041 Fax +81-92-642-3043
> 
> 
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##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow 
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979 
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764 
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk 

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