You're going to need to generate a prep file for the molecule.
Antechamber can do that. The manual explains reasonably well, but ask
if you have difficulty.
Then, in leap:
source leaprc.gaff2
loadamberprep lignin.prep
lignin = loadpdb lignin.pdb
On Fri, Apr 24, 2020 at 3:30 AM Pinky Mazumder <pmazumder67.gmail.com> wrote:
>
> Hi Lachele,
>
> Hope you are well.
>
> I have generated a pdb file of another polymer (lignin) using graphic antechamber. Then, if I want to load it into xleap, what command should I use?
>
>
> Thank you.
>
> Sincerely yours,
>
> Pinky
>
> On Wed, Apr 22, 2020, 7:17 AM Lachele Foley <lf.list.gmail.com> wrote:
>>
>> Don't use pdb4amber. it is already in AMBER format. You also do not
>> need to use reduce.
>>
>> You will need to alter the charge as described at the link I posted
>> above. You must add the charge modification to the leap commands I
>> gave above.
>>
>> On Mon, Apr 20, 2020 at 9:30 PM Pinky Mazumder <pmazumder67.gmail.com> wrote:
>> >
>> > Hi Lachele,
>> >
>> > I have converted the pdb files using the following command:
>> >
>> > pdb4amber -i orig.pdb -o new.pdb --reduce --dry
>> >
>> >
>> > However, I have loaded the pdb files in xleap which is edited by you and have checked that if the total charge are zero or not. I found that the unit hema_TER.pdb is not zero.
>> >
>> > Attached is the screenshot of this. Please find this.
>> >
>> >
>> > How do I solve this?
>> >
>> > Sincerely,
>> > Pinky
>> >
>> > On Mon, Apr 20, 2020 at 1:48 AM Lachele Foley <lf.list.gmail.com> wrote:
>> >>
>> >> What do you mean by "converted"? Do you mean that you added TER cards
>> >> to the PDB file? Did you do anything else?
>> >>
>> >> The way to really check bonding is to generate topology/coordinate
>> >> files (parm7/rst7) and then load them into a viewer like VMD or
>> >> Chimera. When I do that, and output a set of pamr7/rst7 files, the
>> >> bonding looks ok. I don't have xleap at easy access at the moment, so
>> >> I'm can't check the behavior there, but it's not super important.
>> >>
>> >> Note that you will also need to alter the charge on the C atom where
>> >> the MEX is attached. The website does that automatically where it
>> >> can, but there is no standard way to encode charge in a PDB file, so
>> >> if you need to use the PDB file like you are, then you will need to
>> >> adjust charge. The doc is below.
>> >>
>> >> http://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/
>> >>
>> >> I used these commands in tleap:
>> >>
>> >> source leaprc.GLYCAM_06j-1
>> >> m = loadpdb hema_TER.pdb ## I added TER cards to the PDB file you
>> >> sent a couple emails ago
>> >> check m ## this gets tleap to perform some simple checks on your
>> >> molecule, including total charge - should be zero if correct
>> >> saveamberparm m m.parm7 m.rst7
>> >> quit
>> >>
>> >> Then, I loaded them into vmd with:
>> >>
>> >> vmd m.parm7 m.rst7
>> >>
>> >> Make sure that this works by itself, then try to combine this and your
>> >> other molecule.
>> >>
>> >> I've attached the PDB file with the TER cards added.
>> >>
>> >> Let me know if you have other questions.
>> >>
>> >> On Mon, Apr 20, 2020 at 1:05 AM Pinky Mazumder <pmazumder67.gmail.com> wrote:
>> >> >
>> >> > Hi Lachele,
>> >> >
>> >> > Hope you are doing well.
>> >> >
>> >> > I am facing another problem. I have build the hemicellulose chain using glycam carbo builder. so, for loading it in xleap, it needed to be converted.
>> >> >
>> >> >
>> >> > The converted pdb looks fine in vmd. However, when I have loaded it into xleap, I found that the alpha-glucoronic residue have detached from the beta-xylose chains.
>> >> >
>> >> >
>> >> > Attached is the image of vmd as well as xleap. Could you please tell me why this is happening?
>> >> >
>> >> >
>> >> > Thank you.
>> >> >
>> >> > Sincerely,
>> >> > pinky
>> >> >
>> >> > On Sat, Apr 18, 2020 at 2:21 AM Lachele Foley <lf.list.gmail.com> wrote:
>> >> >>
>> >> >> 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
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Pinky, Sharmi
>> >> > AL,US
>> >>
>> >>
>> >>
>> >> --
>> >> :-) Lachele
>> >> Lachele Foley
>> >> CCRC/UGA
>> >> Athens, GA USA
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>> >
>> > --
>> > Pinky, Sharmi
>> > AL,US
>>
>>
>>
>> --
>> :-) Lachele
>> Lachele Foley
>> CCRC/UGA
>> Athens, GA USA
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Fri Apr 24 2020 - 05:00:02 PDT
