AMBER Archive (2009)

Subject: [AMBER] sequence function

From: taufik.alsarraj_at_utoronto.ca
Date: Mon Apr 06 2009 - 12:03:20 CDT

Hello,

I am trying to use the sequence function to connect a dna strand to a
linker to a surface

the function i use in xleap is >system = {dna smcc sur}
all three components have head and tail atoms and there is a *.frcmod
file that describes the parameters not in *leaprc.ff99SB and
leaprc.gaff.
Individually, dna, smcc and sur can run in sander, i tried connecting
dna and smcc only and it works. However, connection all three or smcc
and sur does not work. xleap crashes giving the following error
message, i only attached the end of the error message

+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-O7-SI2-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-O2-SI1-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-O4-SI1-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-O227-SI90-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 142
!FATAL: Message: Atom named H273 from Sur did not match !
!
!ABORTING.

SI1 etc are atom names of an Si type, i am not sure why Add ATOM Types
function is needed as these parameters are defined in my *.frcmod file.

Many thanks,
Taufik

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber