Subject: GROMOS96 parallelisation & glycosylated residue topologies

From: "l.r.cooper" <[email-masked]>
Date: Fri, 14 May 1999 11:59:35 +0100 (BST)

after many a month i have managed to simulate the dynamics of a native
protein with g96.

my parallel implementation does not work with data sets and switch values
which do work in a scalar version. any suggestions? nonbpl array size?
the error message relates to a shake failure- which doesn't occur in
scalar.

i want to describe this modified glycine residue 

po3-o-ch2-ch2o-ch2o-ch2o-ch2o-ch=nh-ch2-co-amino acid2-aa3-
				^   ^
                    schiff's base   alpha carbon of glycine

and the circularized amadori product.

i have abandoned trying to do this by hand. prodrg_serv at embl
creates a gromos87 topology, which i have in hand.

in the /contrib/ directory of gromos96 there is a routine which
translates G87 topologies to G96. the problem is it doesn't get past
reading NRATT number of atoms without an error.

has anyone had a similar experience?

do you have a work around?

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