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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 17 2020 - 08:30:02 PDT
