[gmx-users] apply pH effect on aminoacids

Hi I gave a topology of a protein with pdb2gmx command in next step I change protonation some aminoacids but the topology didn't chage. How could I create new topology? I need to obtain topology protonated aminoacid from other servers? Thanks -- Gromacs Users mailing list * Please search the

[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

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

[gmx-users] question about how to analyze the free energy landscape generated with gmx sham

Dear Gromacs users; I have generated Gibbs free energy landscapes from the two first principal components PC1 and PC2 obtained from Dihedral Principal Component analysis performed using Gromacs. So, now I have a file *"shamlog-1_2.log" *that contain a list of the bins ordered by energy, for

Re: [gmx-users] Lincs warning and Bond length not finite

You have pressure scaling and LINCS convergence issues, suggesting that the starting configuration is far from equilibrium, as well as potentially other issues. Gromos FF is not appropriate for graphene, and neither is turning C-C bonds into LINCS constraints, as set by your 'all-bonds' --

Re: [gmx-users] apply pH effect on aminoacids

Protonation state of the amino acids are set during execution of pdb2gmx and you can choose yourself what their protonation state is using -inter or any of the other options if you don't want to go through all. http://manual.gromacs.org/documentation/current/onlinehelp/gmx-pdb2gmx.html Catch ya,

Re: [gmx-users] [EXTERNAL] Lincs warning and Bond length not finite

How did you set up your graphene sheet originally? Also are you treating the sheet as an infinite sheet (using with periodic molecules)? -Micholas -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Mohamed Abdelaal Sent: Sunday, May 3, 2020 8:40

[gmx-users] Lincs warning and Bond length not finite

Hello everyone, I am simulating the evaporation of non protein molecules on a graphene sheet. I am using gromos force field and hence the lincs constrain are set to all-bonds. I have done the energy minimization and NVT successfully without any warnings. During the NPT equilibiration I got

Re: [gmx-users] [EXTERNAL] Re: Lincs warning and Bond length not finite

OPLS tends to be a common choice for graphene. That being said, if you really want to use gromos (for some reason), be sure (as Alex has stated) to make sure that the graphene edges match across the PBC otherwise do not use PBC (but then be sure to change your electrostatics appropriately and

Re: [gmx-users] conformation tensor

gmx distance -oxyz ? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every