Hi Lachele,
As you said about the combine command. It works.
Thank you so much.
Sincerely,
Pinky
On Fri, Apr 17, 2020 at 9:59 AM Pinky Mazumder <pmazumder67.gmail.com>
wrote:
> Also I do not have the Amber style pdb file. Do I need this for combining
> the two pdb?
>
> Thank you.
>
> Sincerely,
> Pinky
>
> On Fri, Apr 17, 2020 at 2:45 AM Pinky Mazumder <pmazumder67.gmail.com>
> wrote:
>
>> Thank you for your cordial response.
>>
>> Here I have attached the two pdb files of cellulose and hemicellulose.
>>
>> I need to combine those chain as a single pdb so that I can run the
>> relaxation.
>>
>>
>> Thank you again.
>>
>> Sincerely,
>> Pinky
>>
>> On Fri, Apr 17, 2020 at 1:06 AM Lachele Foley <lf.list.gmail.com> wrote:
>>
>>> That usually means you have a bonding issue. You will often need to
>>> make little edits to your PDB file and/or leap commands to get carbs
>>> to be loaded properly.
>>>
>>> Did you download the amber-style pdb file? Can you send me your pdb
>>> file?
>>>
>>> On Fri, Apr 17, 2020 at 1:59 AM Pinky Mazumder <pmazumder67.gmail.com>
>>> wrote:
>>> >
>>> > Hi Lachele,
>>> >
>>> > Thank you for your reply.
>>> >
>>> >
>>> > I have build the hemicellulose using glycam carbohydrate builder and
>>> then I
>>> > am trying to load the pdb file of ''hemicellulose'' using loadpdb
>>> command
>>> > in xleap.
>>> >
>>> > But, It shows the error !FATAL: Message: Atom named C1 from 4LA did
>>> not
>>> > match !
>>> >
>>> > Attached is the screenshot.
>>> >
>>> > Do you have any idea why this is happening?
>>> >
>>> > Any help would be appreciated.
>>> >
>>> >
>>> > Thank you again.
>>> >
>>> >
>>> > Sincerely,
>>> > Pinky
>>> >
>>> > On Thu, Apr 16, 2020 at 3:23 AM Lachele Foley <lf.list.gmail.com>
>>> wrote:
>>> >
>>> > > I usually use tleap rather than xleap, but you should be able to use
>>> > > either. See my previous reply, but also consider the 'combine'
>>> > > command.
>>> > >
>>> > > Learning to use xleap or tleap takes a little time, but the Amber
>>> > > manual does a pretty good job of describing the functions.
>>> > >
>>> > > On Wed, Apr 15, 2020 at 11:14 PM Pinky Mazumder <
>>> pmazumder67.gmail.com>
>>> > > wrote:
>>> > > >
>>> > > > Dear Amber Users,
>>> > > >
>>> > > > I have built cellulose chain using xleap command. On the other
>>> hand,
>>> > > > I have made the chain of hemicellulose using GLYCAM_06 carbohydrate
>>> > > builder.
>>> > > >
>>> > > > Now, I need to put the chain close together.
>>> > > >
>>> > > >
>>> > > > So, my question is, how can I make the both chains closer together?
>>> > > Should
>>> > > > I load the chain of hemicellulose in xleap? If it is, then what is
>>> the
>>> > > > command for this job?
>>> > > >
>>> > > >
>>> > > > Any help would be appreciated. Please forgive me if I am asking
>>> something
>>> > > > silly.
>>> > > >
>>> > > > Thank you.
>>> > > >
>>> > > > --
>>> > > > Pinky
>>> > > > AL,US
>>> > > > _______________________________________________
>>> > > > AMBER mailing list
>>> > > > AMBER.ambermd.org
>>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>>> > >
>>> > >
>>> > >
>>> > > --
>>> > > :-) Lachele
>>> > > Lachele Foley
>>> > > CCRC/UGA
>>> > > Athens, GA USA
>>> > >
>>> > > _______________________________________________
>>> > > AMBER mailing list
>>> > > AMBER.ambermd.org
>>> > > http://lists.ambermd.org/mailman/listinfo/amber
>>> > >
>>> >
>>> >
>>> > --
>>> > Pinky
>>> > AL,US
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
>>> --
>>> :-) Lachele
>>> Lachele Foley
>>> CCRC/UGA
>>> Athens, GA USA
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> --
>> Pinky
>> AL,US
>>
>
>
> --
> Pinky, Sharmi
> AL,US
>
--
Pinky, Sharmi
AL,US
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Received on Fri Apr 17 2020 - 14:30:02 PDT
