Re: [gmx-users] Solvation Free energy using Amber

Ok, thank you for your time. > > > jorge_quint...@ciencias.uis.edu.co wrote: >> Ok Justin, I send You a copy of muy simulation for SFE with two proteins >> + >> water. Look the top file structure. Thanks again. >> > > A quick look at the topologies indicates to me that something is badly > broke

Re: [gmx-users] Solvation Free energy using Amber

jorge_quint...@ciencias.uis.edu.co wrote: Ok Justin, I send You a copy of muy simulation for SFE with two proteins + water. Look the top file structure. Thanks again. A quick look at the topologies indicates to me that something is badly broken. The net charge on each of your protein subu

Re: [gmx-users] Solvation Free energy using Amber

jorge_quint...@ciencias.uis.edu.co wrote: Well, The main reason why I've testedd to obtain solvation free energy (SFE) for toluene is because I want to do it for my future studies related with dimer SFE employing Amber force field with gromacs 4.0. Recently, I've read the tutorial. But, when I

Re: [gmx-users] Solvation Free energy using Amber

Well, The main reason why I've testedd to obtain solvation free energy (SFE) for toluene is because I want to do it for my future studies related with dimer SFE employing Amber force field with gromacs 4.0. Recently, I've read the tutorial. But, when I tried to do the same, I got some errors durin

Re: [gmx-users] Solvation Free energy using Amber

jorge_quint...@ciencias.uis.edu.co wrote: Dear Justin I removed the semicolons but my calculations don't work. The problem is how can I add the other parameters -like bonds, angles and dihedrals- for B-state. I've tried to add it, but I get some problems to obtain the tpr file. Thanks again

Re: [gmx-users] Solvation Free energy using Amber

Dear Justin I removed the semicolons but my calculations don't work. The problem is how can I add the other parameters -like bonds, angles and dihedrals- for B-state. I've tried to add it, but I get some problems to obtain the tpr file. Thanks again. [ bonds ] 1 2 1 --> how can I

Re: [gmx-users] Solvation Free energy using Amber

jorge_quint...@ciencias.uis.edu.co wrote: Dear all. I've tried to calculate solvatin free energy using amber force field and gromacs but unfourtunately I can't include the parameters for B type. Can somebody help me with that, I send you a top file. All of your B-state parameters are comme

[gmx-users] Solvation Free energy using Amber

Dear all. I've tried to calculate solvatin free energy using amber force field and gromacs but unfourtunately I can't include the parameters for B type. Can somebody help me with that, I send you a top file. Best regards, Jorge R. Quintero Grupo de Investigación en Fisicoquímica Teórica y Exp