AMBER Archive (2004)

Subject: Re: AMBER: problems in using glycam

From: Karl N. Kirschner (crux5_11_at_yahoo.com)
Date: Wed Jun 30 2004 - 10:29:37 CDT

Hi Wenchi,
  Below are some attempt to answer your questions.

On Wed, 2004-06-30 at 07:12, Wen-Chi Tseng wrote:
> 1. When I loaded the glycam04EP force field into tleap by typing
> "source /usr/local/amber8/dat/leap/cmd/leaprc.glycam04EP", I got the
> following message.
>
> ----- Source: /usr/local/amber8/dat/leap/cmd/leaprc.glycam04EP
> ----- Source of /usr/local/amber8/dat/leap/cmd/leaprc.glycam04EP done
> Log file: ./leap.log
> Loading parameters: /usr/local/amber8/dat/leap/parm/glycam04EP.dat
> Reading force field mod type file (frcmod)
> Unknown keyword: HW OW in parameter file.
> Unknown keyword: N NA N2 in parameter file.
> Unknown keyword: C C* CA in parameter file.
> Unknown keyword: END
> in parameter file.
> Unknown keyword: END
> in parameter file.
> No mass defined for non-bond atom type: H3 - skipping
> Loading Prep file: /usr/local/amber8/dat/leap/prep/glycam04EP.in.
>
> I quited tleap, and reloaded glycam04 force field instead of the
> long-pair one. Everything turned out to be normal; the error messages
> were gone.
> Is there something wrong with the glycam04EP.dat file? If so, please
> advise how to fix it.

It appears that the format for glycam04EP file is slightly off. We will
correct this shortly and post it on the glycam website
(glycam.ccrc.uga.edu)

> 2. I followed the example in the manual of Amber 8 (p. 26 - 28) to
> construct the man9 molecule of the example. But I got some error
> messages when I typed "set part1 tail part1.2.16" and "part2 =
> sequence { part1 2MA 2MA 1MA }" to set the tail atom of part1 to O3
> of VMB and then to join part1 to the long chain.
>
> ERROR: Comparing atoms C3, H2, O2, C1 to atoms C3, H2, C1, O2
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 121
> !FATAL: Message: Atom C1 is not in the first list
> !
> !ABORTING.
>
> Does the example in the manual contain typos? If so, can
> anyone provide the corrections?

There is a mistake in the manual. The manual, stating "using the
glycam04 parameter, actually has the example of how to build a
polysaccharide using the glycam04EP. This is what it is off a little.
The correct set of command for building a polysaccharide is at the end
of this email.

> 3. I decided to construct a simple sugar, maltose, using glycam04.
> Here is what I did and what I got. It seems that I need to define the
> torsions and charge of the molecule. Can anyone advise how to do this
> and where to get the correct torsion information?
>
> mal = sequence { 1GA 4GA }
> saveamberparm mal mal.top mal.crd

> Checking Unit.
> ERROR: The unperturbed charge of the unit: 0.199000 is not integral.
> WARNING: The unperturbed charge of the unit: 0.199000 is not zero.

This is because our carbohydrates are all reduce - they have a methoxy
functional group at the C1 position instead of a hydroxy group. Adding
the methoxy group. For the alpha anomer of maltose it would be mal =
sequence { OME 4GA 1GA).

> -- ignoring the error and warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Could not find angle parameter: OH - CG - OS
> Could not find angle parameter: CG - OH - CG
> Building proper torsion parameters.
> ** No torsion terms for HO-OH-CG-H2
> ** No torsion terms for HO-OH-CG-OS
> ** No torsion terms for OH-CG-OS-CG
> ** No torsion terms for H1-CG-OH-CG
> ** No torsion terms for H1-CG-OH-CG
> ** No torsion terms for CG-OH-CG-H2
> ** No torsion terms for CG-OH-CG-CG
> ** No torsion terms for CG-OH-CG-OS
> ** No torsion terms for CG-CG-OH-CG
> Building improper torsion parameters.
> total 0 improper torsions applied
> Building H-Bond parameters.
> Parameter file was not saved.

  These will go away with the correct build sequence { OME 4GA 1GA }.

Hope this helps and clarify things. Here is the glycam04 build sequence
for leap:

logFile leap.log
#
#
# Making Branched Carbohydrates
#
# In general, the head atom is set to C1 in each sugar, where the tail
atom
# varies depending on the sugar linkage. For all sugars, the tail atom
is
# specified as the glycosidic oxygen with the largest atomid, i.e. for
the
# 2,3,4, linked sugars the tail atoms would be O4. Therefore, it it
possible
# to build the longest chain according to this convention and then
connect
# the branched portions. Simply changing the tail atom enables a
different
# connection point for the unit, which can then be utilized to sequence
to
# any branched residue/s.
#
#
# Example: Man9
#
# Mana1 - 2Mana1 \
# 3
# Mana1
# 6 \
# Mana1 - 2Mana1 / 6
# ManB-OMe
# 3
# Mana1 - 2Mana1 - 2Mana1 /
#
#
# First, we must load the necessary parameters and prep files
#
source leaprc.Glycam_04
#
# Find the longest chain and use the sequence command to build it
# (See the manual for naming conventions)
#
part1 = sequence { OME VMB 2MA 2MA 1MA }
#
# Now set the tail atom of part1 to O3 of VMB
#
set part1 tail part1.2.9
#
# Join the first branch to the long chain
#
part2 = sequence { part1 VMA 2MA 1MA }
#
# Set the tail atom of part2 to O3 of VMA
#
set part2 tail part2.6.19
#
# Add the last branch
#
man9 = sequence { part2 2MA 1MA }
#
# The basic structure has been built, but it clearly does not have the
optimal
# glycosidic torsion angles.
#
# Set the psi(1-6) torsion to 180 (C1-O6-C6-C5)
#
impose man9 { 2 3 4 } { { C5 C6 O6 C1 180.0 } }
#
# Set the omega angle of 6-linked sugars to 60.0 (O5-C5-C6-O6)
#
impose man9 { 2 3 } {{ O6 C6 C5 O5 60.0 } }
#
# Set the phi angle of all a-linked (not 1-6 linked) sugars to -60.0
#
impose man9 { 4 5 6 7 8 9 10 } { { H1 C1 O2 C2 -60.0 } }
impose man9 { 6 2 } { { H1 C1 O3 C3 -60.0 } }
impose man9 { 9 3 } { { H1 C1 O3 C3 -60.0 } }
# Set the psi angle of all sugars to 0.0
#
impose man9 { 4 5 6 7 8 9 10 } { { C1 O2 C2 H2 0.0 } }
impose man9 { 6 2 } { { C1 O3 C3 H3 0.0 } }
impose man9 { 9 3 } { { C1 O3 C3 H3 0.0 } }
#
# Now we have a reasonable starting structure for AMBER min/md, but we
need
# to save a topology and coordinate file as well as a pdb for later use.
#
saveamberparm man9 man9.top man9.crd
savepdb man9 man9.pdb
#
# Exit the program
#
#quit
#
# For more info visit the GLYCAM website www.glycam.ccrc.uga.edu

Cheers,
Karl

---------------------------------
Karl Nicholas Kirschner, Ph.D.
Assistant Professor of Chemistry
Hamilton College, NY 1323
---------------------------------

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