Vivek,
in your prep file, I did the S->M change for C and deleted the line with
the single "0.0000", then successfully ran the following commands
through tleap:
source leaprc.gaff
loadamberprep cor3.prep
deca = sequence { PO2 PO2 }
saveamberparm deca abc.top abc.crd
savepdb deca abc.pdb
quit
The tleap run created a pdb file I could visualize.
From that inspection it seems that the structure (definition) of your
PO2 entity is not correct at the C-terminal end; maybe your input
structure was corrupt at some point.
I assume that you are aware of the fact that your prep file lacks any
atomic charges at the moment.
A further remark:
Since you used gaff atom types for your system, you will need extra
parameters for the description of the peptide bond to a amino acid
residue, which uses parm14SB or something similar; because your PO2
entity seems to be a mid-chain residue.
(You could simply use a sequence with ACE and NME caps to see that.)
Good luck!
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 21.10.2021 um 07:06 schrieb vivek rabha:
> 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 Fri Oct 22 2021 - 05:30:02 PDT
