Hi Lachele
Forgive me my absent mindedness, for actually i am builiding a glycoprotein
and I wanted to enquire about the errors that i got. These were the *
NET NEGATIVE CHARGE* and *OLD PREP-SPECIFIED IMPROPERS.* So i put the
topic of my mail according to the errors i got then. But before sending
it to AMBER mails i searched the queries made by others to find an answer
for myself, which fortunately i got for the *NET charge* error at least.
But, finally when i sent the mail to amber I forgot to remove the "net
charge" part from the topic of the mail..
Only the WARNING concerning the improper dihedrals was expected to be the
major query!
But thanks to you for explaining how to build an oligosachharide using leap.
The negative charge is not from the sugars, its for the protein..
And the 1VA molecule is simply bound and not actually a part of the
oligosaccharide or the glycoprotein. The WYB and 4YB however are in the
oligosaccharide (a branched one) which i could successfully make using
xleap..
So thanks again Lachele.
And thanks to Bill Ross too for answering my query. By asking about
>>What might be the implications of this (if this is a problem)
>>in the MD simulations (if performed without any changes)?
I was trying to ask whether I would be required to make some changes like
getting newer version of the prep files or some modification elsewhere etc.
and that If I go on without making any such changes anywhere how might this
affect the simulations?
On 7/25/08, Lachele Foley (Lists) <lf.list.gmail.com> wrote:
>
> 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.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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--
sandy_thesmitten
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Received on Wed Jul 30 2008 - 06:07:21 PDT
