does Xleap thinks that all sp2 atoms should have an proper torsion term and
due to this reason its giving only warning ??
regards
sm
---------- Forwarded message ----------
From: Sushil Mishra <sushilbioinfo.gmail.com>
Date: Mon, Mar 8, 2010 at 3:55 PM
Subject: Xleap : Improper torsions applied
To: AMBER Mailing List <amber.ambermd.org>
Hi all;
I have a protein/fucose complex structure, I have changed the naming
convention of alpha-al-me-fucose in to OME (for axygen and methyl carbon)
and 0fA for rest fo the sugar.
I run the xleap by > xleap -s -f leaprc.ff03 ; and then in xleap > source
leaprc_GLYCAM_06
Now after reading it in xleap, I am saving the amber parameters file leap
and the process goes as fallows-
> saveamberparm complex rsl_fuc.prmtop rsl_fuc.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
<0FA 268>: C2 H1 C1 O5
<0FA 270>: C2 H1 C1 O5
<0FA 272>: C2 H1 C1 O5
<0FA 274>: C2 H1 C1 O5
<0FA 276>: C2 H1 C1 O5
<0FA 278>: C2 H1 C1 O5
total 870 improper torsions applied
6 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
CASN 1
CSER 1
CTHR 1
NSER 3
)
(no restraints)
>
When i have a look in leap.log file it shows....
> saveamberparm complex rsl_fuc.prmtop rsl_fuc.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for H-H-N3-H
atoms are: H1 H2 N H3
** Warning: No sp2 improper torsion term for H-H-N3-CT
atoms are: H1 H2 N CA
** Warning: No sp2 improper torsion term for H-H-N3-CT
atoms are: H1 H3 N CA
** Warning: No sp2 improper torsion term for H-H-N3-CT
atoms are: H2 H3 N CA
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for CT-H-N3-H
atoms are: CE HZ1 NZ HZ2
**
**
** same errors !!
**
**
**
** Warning: No sp2 improper torsion term for H1-OS-CG-OS
atoms are: H1 O5 C1 O
** Warning: No sp2 improper torsion term for CG-OS-CG-OS
atoms are: C2 O5 C1 O
old PREP-specified impropers:
<0FA 268>: C2 H1 C1 O5
<0FA 270>: C2 H1 C1 O5
<0FA 272>: C2 H1 C1 O5
<0FA 274>: C2 H1 C1 O5
<0FA 276>: C2 H1 C1 O5
<0FA 278>: C2 H1 C1 O5
total 870 improper torsions applied
6 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
CASN 1
CSER 1
CTHR 1
NSER 3
)
(no restraints)
What am i doing wrong ?? please let me know ?
reg
SM : -)
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Received on Mon Mar 08 2010 - 09:00:02 PST
