Sorry I didn't reply before now. Did you figure it out? Do you still
need help?
On Fri, Apr 17, 2020 at 5:28 PM Pinky Mazumder <pmazumder67.gmail.com> wrote:
>
> 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
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sat Apr 18 2020 - 01:00:02 PDT
