[gmx-users] Glycosylation of ASN
Hi, Have you tried reducing the timestep in mdp? Yes, I tried. But no hope. On Mon, May 4, 2020, 2:52 AM Naba 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 0.03, max 0.13 (between atoms 23 and 24) *>* bonds that rotated more than 30 degrees: *>* atom 1 atom 2 angle previous, current, constraint length *>* 21 22 67.60.1090 0.1090 0.1090 *>* 21 22 67.60.1090 0.1090 0.1090 *>* 21 22 67.60.1090 0.1090 0.1090 *>* 21 22 67.60.1090 0.1090 0.1090 *>* 21 22 67.60.1090 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, 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 0.03, max 0.13 (between atoms 23 and 24) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 21 22 67.60.1090 0.1090 0.1090 > 21 22 67.60.1090 0.1090 0.1090 > 21 22 67.60.1090 0.1090 0.1090 > 21 22 67.60.1090 0.1090 0.1090 > 21 22 67.60.1090 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 > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read
Re: [gmx-users] Glycosylation of ASN
Hi, Have you tried reducing the timestep in mdp? On Mon, May 4, 2020, 2:52 AM Naba 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 0.03, max 0.13 (between atoms 23 and 24) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 21 22 67.60.1090 0.1090 0.1090 > 21 22 67.60.1090 0.1090 0.1090 > 21 22 67.60.1090 0.1090 0.1090 > 21 22 67.60.1090 0.1090 0.1090 > 21 22 67.60.1090 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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Glycosylation of ASN
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 0.03, max 0.13 (between atoms 23 and 24) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 21 22 67.60.1090 0.1090 0.1090 21 22 67.60.1090 0.1090 0.1090 21 22 67.60.1090 0.1090 0.1090 21 22 67.60.1090 0.1090 0.1090 21 22 67.60.1090 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
