[gmx-users] Alinging beta sheets

[Nuno R. L. Ferreira]

Gaurav Porwal <gauravp at che.iitb.ac.in> escreveu:

> Hi,
> 
> >From a secondary structure prediction program, I'm able to get the
> regions in the sequence where helices and beta strands are probably
> present. As helices are independent structures, the whole region can be
> specified as an helix and can be freezed during energy minimization.
> 
> The problem arrives in case of beta strands as two strands have to come
> close in parallel/antiparallel fashion in order to form a sheet.
> 
> Is is possible to construct H bonds in GROMACS such that we can specify
> which residues should be forming the bonds, so that two strands can be
> forced to come close to form a sheet? In this way, beta sheets can
> also be obtained which can later be freezed during energy minimization.
> 

Perhaps distance restraints?

> Kindly reply.
> 
> Thanks.
> 
> Regards,
> Gaurav
> 
> **********************************************************************
> It's amazing what a man can accomplish when he's not worried about who
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> **********************************************************************
> 
>                            Gaurav Porwal
> 		    Senior Undergraduate Student
> 		  Department of Chemical Engineering
>                          IIT Bombay, Powai
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> Alternative Email Id's :-
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-- 
-----------------------------------------------------
Nuno Ricardo Santos Loureiro da Silva Ferreira
Ph.D student
Grupo de Química Biológica
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
Portugal
www.biolchem.qui.uc.pt
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\" Do not worry about your dificulties in mathematics.
   I can assure you that mine are still greater.\"
                                       e=mc2
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