[gmx-users] residue

[Semen Esilevsky]

Hi all,
I know that this question was already discussed, but
could you explain the meaning of this message:

Stepsize too small (7.83488e-07 nm)Converged to
machine precision,
but not to the requested precision (200)

It is Ok if I use larger convergence (like 2000) but
it doesn't work with the values smaller then 300.
What is the optimal value of this parameter?
How to overcome this?

Tnahk you in advance.

--- Xavier Periole <x.periole at chem.rug.nl> wrote:
> Dinesh Pinisetty wrote:
> 
> >
> >
> >Hi all,
> >        Is there anyway to avoid the problem
> because of residues.When I
> >imported a pdb file for Glycerol or methanol etc I
> am getting an error as
> >--- residue is not present in the residue topology
> database.
> >
> I don't know about glycerol but there an .itp file
> specific for
> methanol. Should be in
> the top directory.
> 
> >        I searched in the .rtp of all the force
> fields I could not find the
> >residue which is present in the pdb file.So,I
> thought probably it was
> >mentioned as other name in the .rtp entry and taken
> a list of all the atoms
> >for that missing residue from the pdb file and
> searched for a list of all
> >those atoms in the .rtp entry still I could not
> find the atoms,some atoms
> >were not seen in the whole .rtp entries.it took me
> many hours to do all
> >these.
> >        Now,is it possible to run Md simulation
> with this pdb file using
> >Gromacs as it is not creating topology and gromacs
> files I do not think it
> >is possible.Its going to be problem not only to me
> but all others if there
> >is no conjunction between pdb files and .rtp
> entries in GROMACS.
> >How to solve this problem if anyone can answer
> these questions I will be
> >very grateful to you.
> >Thanks in advance.....................
> >Thanking you,
> >Yours sincerely,
> >Dinesh pinisetty
> >  
> >
> When your protein is not a "classic one", meaning
> with regular residues,
> you either
> are lucky and someone has already work with special
> residue or you have
> to build the
> topology. Neither Gromacs or any program is a press
> botton software and
> you should
> be able to understand and so create your own
> topology ...
> 
> Good luck
> XAvier
> 
> -- 
> ----------------------------------------------
> 
>    Xavier Periole - Ph.D.
> 
>    Dept. of Biophysical Chemistry / MD Group
>    Univ. of Groningen
>    9747 AG Groningen
>    The Netherlands
> 
>    Tel: +31-503634329
>    Fax: +31-503634800
>    email: x.periole at chem.rug.nl
>    web-page: http://md.chem.rug.nl/~periole
> 
> ----------------------------------------------
> 
> 
> 
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