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Hi Dr. Cagnoni,

You can find more information on this on pg. 242 of the Amber manual: http://ambermd.org/doc12/Amber18.pdf

After you load your pdb in tleap, just type: bond PDBNAME.ResidueNumber.AtomName


Example:

source leaprc.GLYCAM_06j-1
source leaprc.protein.ff14SB
glyprot = loadpdb 3rn3_nlink.pdb

bond glyprot.125.O4 glyprot.126.C1 # make inter glycan bonds w/ source and target.
bond glyprot.126.O4 glyprot.127.C1
bond glyprot.127.O6 glyprot.128.C1
bond glyprot.127.O3 glyprot.129.C1

addions glyprot CL 0
solvateBox glyprot TIP3P BOX 8
savepdb glyprot 3nr3_glycan.pdb
saveamberparm glyprot 3nr3_glycan.top 3nr3_glycan.crd
quit


Kind regards,

Aarya Venkat

Biochemistry PhD Student, Kannan Lab

University of Georgia

https://arikat.github.io/


From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf of Alejandro Cagnoni <[log in to unmask]>
Sent: Tuesday, May 14, 2019 10:00 AM
To: [log in to unmask]
Subject: Re: [AMBER] tleap error in reading structure generated from GLYCAM web
 
Hi Lachele

Thank you very much. If you could please help me with the BOND command, I'd really appreciate it. If not, where can I find the tleap docs?

Thanks again

Alejandro

On Tue, May 14, 2019 at 1:30 AM Lachele Foley <[log in to unmask]> wrote:
Hi!

You have to issue explicit BOND commands in tleap to connect the
residues back together after adding the TER cards.  If you need help
doing that, just say, but it's pretty easy, and there are good
examples in the tleap docs.

On Mon, May 13, 2019 at 12:30 PM Alejandro Cagnoni
<[log in to unmask]> wrote:
>
> Hi.
>
> How are you? I'm following a thread from a couple of years ago. I've been having problems with branched oligosaccharide structures (generated from glycam web) and tleap (Amber). There is a problem with the conncetions of the atoms.
>
> I've seen that Lachele Foley recommended to add "TER" cards on the pdb file. However, by doing so, even if I've solved the tleap problem, I have problems when minimizing the structure with sander (Amber). The monosaccharides don't remain bound to each other. Could you please help me solve this issue?
>
> Thank you very much.
> Best regards.
>
> --
> Dr. Alejandro J. Cagnoni
>
> Instituto de Biología y Medicina Experimental
> Consejo Nacional de Investigaciones Científicas y Técnicas
> Buenos Aires (1425), Argentina
> (011)47832869. int. 204



--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA


--
Dr. Alejandro J. Cagnoni

Instituto de Biología y Medicina Experimental
Consejo Nacional de Investigaciones Científicas y Técnicas
Buenos Aires (1425), Argentina
(011)47832869. int. 204