[gmx-users] how to include Fe-S topology in .rtp file

hi all...   I am simulating a protein with Fe-S cluster. What is the protocol for generating a .rtp file with Fe-S topology...As i am using ffG43a1 forcefield.. i searched FFG43a1bon.itp file for Fe-S bond, angle and dihedral type... but it is not there..what i should do?..   If anyone have the

[gmx-users] how to include ionic strength

Dear gromacs users,   I am simulating a protein which works in salt solution within cell. I have to include 4M salt (say, NaCl) to the simulation box. How can i include such ionic strength? Please outline me the procedure.   Thanks in advance. Amrita Paul     Cricket on your mind? Visit t

[gmx-users] how to do MD simulation of protein with Fe-S cluster

Dear Gromacs users,   I am currently working on Dynamic simulation studies using GROMACS software. In my current work I want to do simulation of a protein containing Fe-S cluster. If i directly do through pdb2gmx then it is giving a error massage like "FES in not included in .rtp file". Regardin

Re: [gmx-users] about md simulation

Dear colleagues, I am simulating a phosphorylated protein embedded in waterbox. When I try running mdrun, I get a LINCS warning. Does this mean that I have go back to the CG-EM step and use the double precision libs? The md.log file reads: Initializing LINear Constraint Solver number of constr

[gmx-users] about md simulation

Dear colleagues, I am simulating a phosphorylated protein embedded in waterbox. When I try running mdrun, I get a LINCS warning. Does this mean that I have go back to the CG-EM step and use the double precision libs? The md.log file reads: ... Initializing LINear Constraint Solver number