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GLYCAM-L  December 2017

GLYCAM-L December 2017

Subject:

how to generate paramaters for GlcNH3 oligodsaccharide

From:

Tarsis Gesteira <[log in to unmask]>

Reply-To:

Users of GLYCAM & GLYCAM-Web <[log in to unmask]>

Date:

Sun, 10 Dec 2017 10:23:42 -0500

Content-Type:

text/plain

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text/plain (24 lines)

Hi all,

While trying to build a hexasaccharide using leap and GlcNH2_and_GlcNH3.prep.

 source leaprc.GLYCAM_06j-1
 loadamberprep GlcNH2_and_GlcNH3.prep
 loadamberparams glcnh3.frcmod
 glycan = sequence { ROH 4ZB 0YNP }
 set glycan tail glycan.3.O4
 glycan = sequence {glycan 4ZB 0YNP }
 saveAmberParm glycan glycam.prmtop glycam.crd
 savepdb glycan glycam.pdb

 I was told that I need to delete the HO4 and alter the charge, as I was getting this error:

> Checking Unit.
> ERROR: The unperturbed charge of the unit: 0.194000 is not integral.
> WARNING: The unperturbed charge of the unit: 0.194000 is not zero.

May I get some help on how to properly do this?

Thanks in advance,

Tarsis