I'm sorry for the unclear questions,,,as a beginner it is difficult for me
to found where is mistake.
I'm just trying to follow the manual and procedure
1) the command i used in tleap to create .top and .crd is
source leaprc.gaff
loadamberprep cor3.prep
deca = createunit deca
deca = sequence {PO2 PO2 PO2}
desc deca
check deca
charge deca
alignaxes deca
saveamberparm deca abc.top abc.crd
savepdb deca abc.pdb
quit
2) it shows some warning after loading my prep file
Warning: 1 of 56 atoms missing charges on atoms lines
3) and if i go forward
after alignaxes deca it shows
ContainerCenterAt(): Skipping atom w/ unknown position: O:O
ContainerCenterAt(): Skipping atom w/ unknown position: O:O
(I visualized in VMD the two oxygen is not forming bond with any atom )
---> i checked all the connection in my prep file but everything is okay
from my side ...i'm unable to find the mistake
4) at last quit
Quit
Exiting LEaP: Errors = 0; Warnings = 19; Notes = 0.
please help me!!!!!!!!!!!!!!!!
Thanking You
Vivek Rabha
On Wed, Oct 20, 2021 at 7:44 PM Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> Vivek,
>
> I'm sorry to learn that my suggestion was not successful.
>
> However, it is hard to help you without knowing the exact commands you
> issued, learning the verbatim error messages, and having all the files
> involved.
>
> Best,
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg
> Germany
>
>
> Am 20.10.2021 um 12:41 schrieb vivek rabha:
> > Anselm sir
> > Thank you for the reply
> > I tried already with M also.... but its showing same problem not
> connected
> > at the correct position
> >
> > On Wed, Oct 20, 2021 at 3:57 PM Dr. Anselm Horn <anselm.horn.fau.de>
> wrote:
> >
> >> Vivek,
> >>
> >> a quick guess:
> >> Change the carbonyl atom line entry (54) in your prep file by
> >> substituting the 'S' by 'M', and try using it again.
> >>
> >> Maybe this helps (I did not visualize your structure or had a closer
> >> look into.)
> >>
> >> Best regards,
> >>
> >> Anselm
> >>
> >> Bioinformatik | NHR.FAU
> >> Friedrich-Alexander-Universität Erlangen-Nürnberg
> >> Germany
> >>
> >>
> >> Am 20.10.2021 um 11:58 schrieb vivek rabha:
> >>> ---------- Forwarded message ---------
> >>> From: vivek rabha <rabhavustm96.gmail.com>
> >>> Date: Wed, Oct 20, 2021 at 3:24 PM
> >>> Subject: topology file and co-ordinate file making by amber tool
> >> (gaff.dat)
> >>> To: <amber.ambermd.org>
> >>>
> >>>
> >>> sir
> >>> I am attaching my prep file plz help me in searching where is the
> >> error?
> >>> I tried many times but it's showing the same error!
> >>>
> >>> The problem is C=O terminal group connection in CA carbon
> >>> Its not connected in the correct position.
> >>>
> >>> and please let me know if my questions is not clear??
> >>>
> >>>
> >>>
> >>> _______________________________________________
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> >>>
> >>
> >>
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Received on Wed Oct 20 2021 - 22:30:02 PDT
