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GLYCAM-L  July 2017

GLYCAM-L July 2017

Subject:

SO3 group bond type for GLYCAM in LAMMPS - reg.

From:

Naveen Kumar Vasudevan <[log in to unmask]>

Reply-To:

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

Date:

Wed, 12 Jul 2017 17:14:29 -0400

Content-Type:

text/plain

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Parts/Attachments

text/plain (22 lines)

Dear GLYCAM users,

I am trying to simulate interaction of polymers with sulphated cellulose, I observed that when I convert the .top and .crd file from amber to a LAMMPS data file, The sulphate group has the same bond type for both single bonded and double bonded oxygen atoms.

From the parameter file, the definition for the bond is as follows

S -O2 620.0 1.440 K calculated from methyl sulphate (eqm value from THEOCHEM 395/396 (1997) 107-122)

Residue info from PREP file.

SO3 INT 0
CORRECT OMIT DU BEG
-0.8370
1 DUMM DU M 0 -1 -2 0.000 0.000 0.00 0.0000
2 DUMM DU M 1 0 -1 0.500 0.000 0.00 0.0000
3 DUMM DU M 2 1 0 1.296 74.264 0.00 0.0000
4 S1 S M 3 2 1 10.884 119.491 -167.81 1.2450
5 O1 O2 E 4 3 2 1.446 106.410 -102.07 -0.6940
6 O2 O2 E 4 3 2 1.437 128.086 115.25 -0.6940
7 O3 O2 E 4 3 2 1.446 70.631 7.86 -0.6940

Shouldn’t these single and double bonds have different bond types ?

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