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.

 

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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Naveen Kumar Vasudevan, Graduate student,
The Xi Research Lab,
Dept. of Chemical Engineering, McMaster University,
JHE- 296, 1280 Main St. W., Hamilton, ON L8S 4L7, Canada
Email: [log in to unmask] ; Tel: +1(647) 629-1562
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