[gmx-users] Re: Glutamate to Alanine Mutation

Prof Mobley, Sorry to bother you, but do you have any suggestions for my previous post? Thanks again, Sai On Sun, Mar 31, 2013 at 9:52 PM, Sai Kumar Ramadugu wrote: > Dear Prof Mobley, > > I have some additional questions in understanding the free energy > calculations. > &g

[gmx-users] Re: Glutamate to Alanine Mutation

lambda=0 and lambda=1) but somewhat larger spacing between 0.1 and 0.9. How does g_bar handle this? Is the integration and error analysis done correctly even when the lambda spacing may be different at different lambda values? Thank you for your time. Regards Sai On Tue, Dec 4, 2012 at 5:27 PM

Re: [gmx-users] carbohydrate forcefield in gromacs

As far as I know, Glycam06 (AMBER) force field is not included in gromacs4.5.5. If you want you can use amb2gmx.pl script that is available online or from Erin Sorin's website at CSU @ Long Beach. Remember that if you want to use GLYCAM06, its better to use AMBER ff99SB or ff03 or the recent ff12

[gmx-users] DelG of LJ Transformation Negative Glu--->Ala Mutation

Hi Gmx Community, I am doing Glutamate to Alanine mutation in presence and absence of a ligand. The Coulomb transformation is yielding the following results: Glu--->Ala + ligand = 790.109 kJ/mol Glu--->Ala + no ligand = 787.33 kJ/mol During the LJ transformation Glu--->Ala + ligand = - 24.87 kJ/m

Re: [gmx-users] FEP

Hi Fabian, I am trying something similar with Glutamate to Alanine mutation. Does your dummy atoms i.e., DUM1 have a value of 0.0 for sigma and epsilon during all three steps or only in step 2? Thanks for the time, Sai On Thu, Apr 26, 2012 at 10:43 AM, Fabian Casteblanco < fabian.castebla...@gma

[gmx-users] Re: Thermodynamic Integration Glu -> Ala Mutation

Any suggestions on this topic? Thanks again for your time. Dear Gromacs Users, > I am trying to find out the relative free energy difference of binding of > a ligand with wild type protein (Glutamate residue) and mutant protein > (Alanine residue). > > For charge part of the mutation, this is wha

[gmx-users] Thermodynamic Integration Glu -> Ala Mutation

Dear Gromacs Users, I am trying to find out the relative free energy difference of binding of a ligand with wild type protein (Glutamate residue) and mutant protein (Alanine residue). For charge part of the mutation, this is what I'm planning to do: ; residue 40 GLU rtp GLU q -1.0 552 opls

[gmx-users] Glutamate Chi1 Dihedral Not Symmetrical?

Dear Gromacs Users, I am trying to plot the Ryckaert-Bellemans energy for rotating the chi1 dihedral of glutamate in protein. I tried to change the ch1 dihedral from 0-360 degrees at increments of 1 degree and saved the pdbs. Then I used the pdb's to obtain the corresponding gro files and a single

[gmx-users] Free Energy calcualtions

Hi Gromacs Users, I want to mutate a glutamate in my protein to alanine in presence of a ligand. With glutamate, the protein charge is -3. To neutralize the system, I added 3K+ ions. Now when I mutate GLU to ALA, the charge in state_B will be +1 (protein -2 + 3K+). Right now I'm in the charge part

Re: [gmx-users] Half double pair list method in GROMACS [update]

Hi Stephane & Chris, I followed all the threads posted by you two. I have a protein using ff99SB and GLYCAM for sugars. I have a disaccharide bound to protein. In xleap of AMBERTOOLS, I use the GLYCAM and ff99SB to generate the topology and coordinate files. I did the tests as Chris' original posts

Re: [gmx-users] pulling force vs free energy

I agree with Justin. I have tried myself several SMD simulations for ligand binding studies. I tried 500 simulations and not sure if they are enough. Further, the path dependence is very important part. For different paths that you can try, look at McCammon group's paper in JACS 128, 3019-3026. The

Re: [gmx-users] How to calculate work

Hi Sanku, I was using the pullf.xvg and multiplying it with pulling rate and time. f*v*dt = W and getting the total work for each SMD simulation. I'm not sure if this is the best/correct way to do it. But from original Jarzynski's article (PRL (2007) 78(14), 2690-2693) this is what I deduced. I as

[gmx-users] Jarzynski and PMF

Dear All, I have tried to calculate the free energy of binding using Jarzynski equality. I employed the following procedure. --I did force pulling simulations along Z-direction as exemplified in Justin's umbrella sampling simulations. I did 50, 250 and 500 pulling simulations to test the converge

[gmx-users] PMF for Carbohydrate-Protein

Dear All, I'm running set of umbrella sampling simulations to get the PMF of a disaccharide binding to a protein. I followed the tutorial provided by Justin and changed the values of necessary parameters according to my system. The mdp file for umbrella sampling simulations is as follows: -

Re: [gmx-users] soft-core

Hi Well the tutorial in the following website has mentioned about the importance of sc_alpha and sc-power. Also the manual gives you more information. http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial. Regards Sai On Sun, Jun 13, 2010 at 6:56 PM, Justin A. Lemkul wrote: >

Re: [gmx-users] PBC

Hi Morteza, I had this problem when I was running a trimeric protein attached to an oligosaccharide. *I have used the following command:* * * *trjconv -s .tpr -f .xtc -o -boxcenter tric -pbc mol* * * *but it is not working.* Do the following. It worked for me. In the first round, run

Re: [gmx-users] Thr -> Met in TI calculation

Hi Fancy, The following link shows the change from p-cresol to Toluene. So follow the steps in the same by converting threonine to methionine. http://compbio.chemistry.uq.edu.au/education/Free-Energy_Course/0.introduction.html Regards Sai 2010/6/5 fancy2012 > Dear GMX users, > > I want to c

Re: [gmx-users] tutorial of free energy calculations

HI Its not working for me either. But for free energy tutorials using GROMACS, I think the one written by Prof Mobley is like Bible. The link is as follows: http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial But the one written by Prof Alan Mark (who is now in Queensland Univ

[gmx-users] Wrapping molecules for octahedron box

Dear Gromacs Users, I have a simulation of a protein in Truncated Octahedron box. I want to calculate the water residence times and mean square displacements (of water) around the active site residues. We developed our own algorithm for doing the same. In earlier simulations I had cubic box and

[gmx-users] Large dVpot/dlamda values at lambda = 1

Hi All, I'm trying to run free energy simulations for a linkage change in an oligosaccharide when bound to its protein. The linkage changes from beta 1-4 to beta 1-3. I followed the tutorial by Prof Mobley. For the lambda values I took 0 to 1 at intervals of 0.05. The values of dVpot/dlambda fro

[gmx-users] Free Energy Calculations for linkage change in disaccharide

Dear All, In my previous email the text in the message was not shown. Thats why I'm writing this again. I request to see the attachment of earlier message. I'm sorry for this!! I have an disaccharide bound to a C-type lectin. The sequence of disaccharide is beta-galactose1-4beta-GlcNAc. The 3

[gmx-users] Free Energy Calculations for linkage change

Dear All, I have an disaccharide bound to a C-type lectin. The sequence of disaccharide is beta-galactose1-4beta-GlcNAc. The 3'OH and 4'OH of beta-galactose coordinate to the Ca2+ at the active site. FRET experiments have shown that if the disaccharide linkage is changed to beta-galactose1-3bet

[gmx-users] free energy calculations for two ligands

Dear All, I have a trimeric protein system which binds to two different ligands. The ligands are oligosaccharides. The difference between the two is first ligand has beta 1-4 linkage and the second ligand has beta 1-3 linkage between Galactose (Gal) and N-Acetyl Glucosamine (GlcNAc). Since the l