AMBER Archive (2009)

Subject: Re: [AMBER] makeDIST_RST: no map function for ambiguous restraint

From: Peter Varnai (p.varnai_at_sussex.ac.uk)
Date: Mon Jun 01 2009 - 14:49:36 CDT

Dear David,

> What you describe should work, but something look amiss in the code to me.
> Try changing line 751 of makeDIST_RST.c from
>
> sscanf( rtyp, "%s", map[nm].rtyp );
>
> to
>
> sscanf( "AMB", "%s", map[nm].rtyp );
>
> You should probably also post your files if this doesn't fix things. You
> might also try adding the "-debug" flag to get more copious output.

this worked as expected, thanks very much.

just a note to say that using the resid and atom names in the
restraint file like: iat=1,1, atnam="H5","H6", iresid=1,... work well
but a similar syntax for a group of atoms is not recognized properly
by amber10; when igr1 is used for the residue number and grnam for
atoms names (iresid=1 and iat<1) only the first atom is recognised
from the group and hence one must use atom numbers instead (this is
also what makeDIST_RST does). Probably the new 'restraint' syntax
should be used in amber10 anyways.

Best regards,
Peter

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