AMBER Archive (2008)

Subject: Re: AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP

From: Lachele Foley (Lists) (lf.list_at_gmail.com)
Date: Fri Jul 25 2008 - 09:47:54 CDT

Regardign the torsions, the format of the input files has changed. I
doubt that, in itself, is an issue.

The non-integral charges, however, is likely to indicate a significant
problem. Typically, it indicates that the residues are not named
and/or terminated properly or that the structure doesn't make the sort
of chemical sense one might expect. Can you tell me the sugar you are
trying to build? If it contains only the residues WYB, 1VA and 4YB,
then there may be a problem. For example, the residue 1VA is only
useful for 1-1 (type) connections. Did you intend to use 0VA instead?

I just built a small, complete, sugar molecule containing those three
residues. I used these commands (in a very recent version of leap):

source leaprc.GLYCAM_06
m1 = sequence { 1VA WYB }
set m1 tail m1.2.O3
m1 = sequence { m1 4YB 0GA }
set m1 tail m1.2.O4
m1 = sequence { m1 0MA }
savepdb m1 m1.pdb
saveamberparm m1 m1.top m1.crd

Please note: as I mentioned above, the first linkage ("sequence { 1VA
WYB }") is a 1-1 linkage, which is very infrequently desired. This is
why I asked earlier if you intended to use 0VA (which would have been
1VA in an old naming system, a fact which frequently causes
confusion).

When I built the molecule, leap gave complaints about the prep file
formatting, like it did for you, but it did not complain about
charges. Note in the output below, that despite complaining about the
torsions, it does say it applied them. I also got what appear to be
valid crd and top files. I loaded them into VMD to test, and the
molecule looks reasonable.

...
Writing pdb file: m1.pdb
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:
 <4YB 3>: C2 C2N N2 H2N
 <4YB 3>: CME N2 C2N O2N
 <1VA 1>: C2 C2N N2 H2N
 <1VA 1>: CME N2 C2N O2N
 <WYB 2>: C2 C2N N2 H2N
 <WYB 2>: CME N2 C2N O2N
 total 6 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.
 (no restraints)

Let me know if you continue to have difficulty.

:-) Lachele

On Fri, Jul 25, 2008 at 6:04 AM, Sandeep Kaushik
<sandy.thesmitten_at_gmail.com> wrote:
> Hi AMBER users,
> I am using AMBER_9 ( Glycam04) and i got a warning about the improper
> torsional angles from xleap while using GlcNac & GalNac sugar units. The
> xleap output is as follows :
>
>
>> saveamberparm ec e2is_g.top e2is_g.crd
> Checking Unit.
> ERROR: The unperturbed charge of the unit: -12.710158 is not integral.
> WARNING: The unperturbed charge of the unit: -12.710158 is not zero.
> -- ignoring the error and warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
>
> old PREP-specified impropers:
> <WYB 242>: C2 C2N N2 H2N
> <WYB 242>: CME N2 C2N O2N
> <4YB 244>: C2 C2N N2 H2N
> <4YB 244>: CME N2 C2N O2N
> <1VA 249>: C2 C2N N2 H2N
> <1VA 249>: CME N2 C2N O2N
>
> total 1524 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
>
> CGLU 2
> NVAL 2
> )
> (no restraints)
>>
>
>
> What does the message "old PREP-specified impropers" mean?
> Are there possible corrections that can be made in this regard?
> What might be the implications of this (if this is a problem) in the MD
> simulations (if performed without any changes)?
>
> Kindly direct me to the possible solutions.
>
> Sandeep
> 

-- 
:-) Lachele
Lachele Foley
CCRC/UGA
2-0263
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