[gmx-users] Glycosylation of ASN

[Naba]

Hi,

Have you tried reducing the timestep in mdp?

Yes, I tried. But no hope.


On Mon, May 4, 2020, 2:52 AM Naba <nabajyoti.goswami at gmail.com
<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>>
wrote:

>* 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.
*>>* Regards,
*>* Naba*


On Mon, 4 May, 2020, 02:51 Naba, <nabajyoti.goswami at gmail.com> wrote:

> 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.
>
> Regards,
> Naba
>
>
> Nabajyoti Goswami
>
> Research Associate
> Bioinformatics Infrastructure Facility
> Department of Animal Biotechnology
> College of Veterinary Science
> Khanapara,Guwahati 781022
> Assam, India
>