[gmx-users] Glycosylation of ASN

Naba nabajyoti.goswami at gmail.com
Sun May 3 23:22:10 CEST 2020

Dear users and developers,

I have spent extensive amount of time to model glycosylated ASN residues
covalently linked with N-ACETYL-D-GLUCOSAMINE (NAG) in a glycoprotein using
Amber99SB-ILDN force field. Though there may be easy way to do this
with CHARMM-GUI, I want it for Amber force field for maintaining
consistency of force field usage with respect to the other sets of
simulations I have performed already.

I have gone through several post on this and planned to give a try. So,
I've extracted a pair of covalently bound ASN and NAG from the PDB file
where they present. I have generated the NAG topology parameters using
GLYCAM_06j-1 force field in Tleap and ACPYPE. I updated aminoacids.rtp,
ffbonded.itp and all required files as instructed in the manual section 5.6
and it was successful in equilibrations. After completion of NVT and NPT
successfully for 500 ps each, around 7 ns of the production MD, I am
encountered with warnings and ultimately fatal error like following:

Step 3869783, time 7739.57 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000003, max 0.000013 (between atoms 23 and 24)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     21     22   67.6    0.1090   0.1090      0.1090
     21     22   67.6    0.1090   0.1090      0.1090
     21     22   67.6    0.1090   0.1090      0.1090
     21     22   67.6    0.1090   0.1090      0.1090
     21     22   67.6    0.1090   0.1090      0.1090

for many steps

and then

step 3869795: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Segmentation fault      (core dumped)

I checked it repeatedly by minimizing the structure several times using
other software including a series of vacuum minimization with
GROMACS-2019.5 using steepest descent and conjugate gradient minimizers.
But no success.

Please try to give a way to resolve it. If possible.


Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India

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