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.gosw...@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 > -- 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.