Re: [gmx-users] About topology construction for Cyclic peptide

On 17/09/2012 11:50 AM, vidhya sankar wrote: Dear Mark, Thank you for your reply I have used the peptide FLF For that pdb2gmx construct topology successfully with -ter choosing any thing for both terminal. OK, well you can work with that topology as your

[gmx-users] Elastic Network Model -harmonic pot

Hi all, I am trying to build an elastic network model using only C-alpha atoms . Potential energy function contains only bond stretching energy term rest like angle,dihedral and non bonded are not included. I use bond function type(f.tp = 6) ,i.e. is harmonic bond potential . The

Re: [gmx-users] Rotated protein

Hi, Your pdb input (protein.pdb) is misformatted. Note that a pdb file is fix-format and that your residue sequence number is misaligned. As a consequence the last digit is not read for two digit residues. Erik 15 sep 2012 kl. 07.56 skrev Shima Arasteh: Sorry for unclear explanation. 1.

Re: [gmx-users] Rotated protein

Thanks dear Erik.   Sincerely, Shima - Original Message - From: Erik Marklund er...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, September 17, 2012 2:05 PM Subject: Re: [gmx-users] Rotated protein Hi, Your pdb input (protein.pdb) is

Re: [gmx-users] Topology and mdp file for coupling vdw and coulombic interactions for running FE calculations using BAR

On 9/16/12 10:45 PM, Sonia Milena Aguilera Segura wrote: Hi, I'm preparing my mdp and topology files for running free energy calculations using BAR method. I´m using Justin Lemkul's tutorial as a reference (You can find it here

[gmx-users] permittivity value

Friends, I am interested in setting the permittivity of the external surface. With the previous posting in the forum, i am able understand the meaning of the epsilon_surface parameter. I would like to know if someone could suggest me some articles that address the role of this parameter. Thanks,

[gmx-users] visualize trajectory

Hi , Which software is used to visualize a large mdrun output? For example 60 GB trajectory file.   Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

[gmx-users] Regarding RMSD graph nalysis

Dear gromacs users I run 20 ns MD simulation for protein mutant complexes. In RMSD analysis at ~9 ns sudden increase in the deviation was observed from 0.2 nm to 1.7 nm and immediate fall was observed. I rerun the 20 ns simulation for the same molecule with same procedure. While analyzing the

[gmx-users] charge calculation........

Dear All, I want to have one of tyrosine residues in my protein to be unprotonated. I am using amber force field for the simulation. But in aminoacid.rtp there is no entry for the unprotonated one. So I am adding it by myself in to the .rtp file. Now I am bit confused with the charge

Re: [gmx-users] visualize trajectory

On 9/17/12 6:57 AM, Shima Arasteh wrote: Hi , Which software is used to visualize a large mdrun output? For example 60 GB trajectory file. I think you should probably have a look at http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume before proceeding. There

Re: [gmx-users] Regarding RMSD graph nalysis

On 9/17/12 7:02 AM, naga sundar wrote: Dear gromacs users I run 20 ns MD simulation for protein mutant complexes. In RMSD analysis at ~9 ns sudden increase in the deviation was observed from 0.2 nm to 1.7 nm and immediate fall was observed. I rerun the 20 ns simulation for the same molecule

Re: [gmx-users] Resuming of calculation from last *.cpt

Dear all, I have read few papers regarding the photo dissociation event such as Myoglobin heme-ligand bond deletion to induce the photodissociation in MD simulation. Could you please tell me the procedure how can i perform the photodissociation mechanism in Gormacs and which force field have to

Re: [gmx-users] charge calculation........

On 17/09/2012 10:01 PM, tarak karmakar wrote: Dear All, I want to have one of tyrosine residues in my protein to be unprotonated. I am using amber force field for the simulation. But in aminoacid.rtp there is no entry for the unprotonated one. So I am adding it by myself in to the

[gmx-users] charge calculation........

Hi Since you want to use the AMBER force for your calculations, you will need to compute the RESP charges for your new residue (unprotoned TYR) and add the charges in your *rtp file. To compute the charges, you can use the RED.Server (http://q4md-forcefieldtools.org/REDS/). It is not easy,

[gmx-users] DNA MD PROBLEM

Hello, This is Anik Sen from India. Am using Gromacs 4.5.5. to do some calculations on solvation and ligand binding interactions with DNA. I have some questions regarding the problem. As water is present in the system, so according to the manual the define in the .mdp file must be

Re: [gmx-users] DNA MD PROBLEM

On 9/17/12 1:06 PM, Anik Sen wrote: Hello, This is Anik Sen from India. Am using Gromacs 4.5.5. to do some calculations on solvation and ligand binding interactions with DNA. I have some questions regarding the problem. As water is present in the system, so according to the

[gmx-users] Re: Topology and mdp file for coupling vdw and coulombic interactions for running FE calculations using BAR

Hi Justin, So, are you saying that I should use my topoly file with all the original charges for both none-vdw and vdw-vdw-q calculations? I understand that the couple-lambda* setting dictate which parameters are involved in both calculations. However, in your tutorial you set all charges to

Re: [gmx-users] Re: Topology and mdp file for coupling vdw and coulombic interactions for running FE calculations using BAR

On 9/17/12 3:38 PM, Sonia Aguilera wrote: Hi Justin, So, are you saying that I should use my topoly file with all the original charges for both none-vdw and vdw-vdw-q calculations? I understand that the couple-lambda* setting dictate which parameters are involved in both calculations.

[gmx-users] Regarding Pulling simulation:To study the base flipping of the thymine

You can do this with the pull code. To do so, you need to define some sort of order parameter for which you have the base flipped in at one extreme and the base flipped out at the opposite extreme. There are lots of ways to do this and, unfortunately, there is no way to know what the best order