[gmx-users] Re: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology

hello justin, I got one more error, please help me out again. I got the em.gro instead of confout.gro. I reached an area per lipid of ~52 Å2 for POPE bi layer. Next i tried to add ions to the system after solvating with water. i get the following error. Program grompp, VERSION 4.5.4 Source

Re: [gmx-users] Re: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology

On 10/08/2012 5:28 PM, leonines wrote: hello justin, I got one more error, please help me out again. I got the em.gro instead of confout.gro. I reached an area per lipid of ~52 Å2 for POPE bi layer. Next i tried to add ions to the system after solvating with water. i get the following

[gmx-users] Empirical potential for Pi stacking interactions?

Dear Gromacs users, I am currently looking for an empirical potential for pi stacking interactions. Something like the Leonard Jones potential, or the Mayo potential for hydrogen bonds. I was wondering if something like that exists for pi stacking interactions? I am not really looking for

Re: [gmx-users] Re: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology

On 8/10/12 12:57 AM, Bhavaniprasad.V wrote: hello justin, I got one more error, please help me out again. I got the em.gro instead of confout.gro. I reached an area per lipid of ~52 Å2 for POPE bi layer. Next i tried to add ions to the system after solvating with water. i get the following

[gmx-users] How it possible find detail way for start preparing INPUT files for simulation of Hypoxanthine (aq) solution by Gromacs

Dear Gromacs workers, I will decide simulate the system of Hypoxanthine (which is rather similar to Guanine) in water solvent. as you know, for this molecule, the force field parameter is not defined in Gromacs database. at this time, people advice contracting of *.itp file for new molecule. but

Re: [gmx-users] How it possible find detail way for start preparing INPUT files for simulation of Hypoxanthine (aq) solution by Gromacs

On 8/10/12 7:14 AM, Mohammad Hossein Kowsari wrote: Dear Gromacs workers, I will decide simulate the system of Hypoxanthine (which is rather similar to Guanine) in water solvent. as you know, for this molecule, the force field parameter is not defined in Gromacs database. at this time,

[gmx-users] PMF - Protein-Me​brane

Hi All, I have a question regards to PMF: Consider we are sure one protein will bind to membrane after 100ns in MD run and make a complex. Instead of pulling protein to membrane to calculate PMF, can we start from last configuration of protein-membrane complex and pull out protein to separate

Re: [gmx-users] PMF - Protein-Me​brane

On 8/10/12 11:18 AM, dariush wrote: Hi All, I have a question regards to PMF: Consider we are sure one protein will bind to membrane after 100ns in MD run and make a complex. Instead of pulling protein to membrane to calculate PMF, can we start from last configuration of protein-membrane

[gmx-users] Protein-ligand - genion error

Dear All, I have been trying to perform simulation for a Protein and Ligand complex. However, when I run genion, I get an error The solvent group SOL is not continuous: index[37530=23341, index[3754]=23606. I remember reading someone posting a similar problem and the solution was provided,

Re: [gmx-users] Protein-ligand - genion error

On 8/10/12 1:05 PM, Ankita naithani wrote: Dear All, I have been trying to perform simulation for a Protein and Ligand complex. However, when I run genion, I get an error The solvent group SOL is not continuous: index[37530=23341, index[3754]=23606. I remember reading someone posting a

[gmx-users] Umbrella sampling

Good morning, I am trying to run an umbrella sampling simulation, my system is a complex of two proteins. I have a couple of questions: 1. i don't know which is the purpose in defining the charge of each protein end 2. When i check the topol.itp file of the reference molecule i realized that it

Re: [gmx-users] Umbrella sampling

On 8/10/12 1:14 PM, Paula Andrea Delgado Pinzon wrote: Good morning, I am trying to run an umbrella sampling simulation, my system is a complex of two proteins. I have a couple of questions: 1. i don't know which is the purpose in defining the charge of each protein end A net charge is a

Re: [gmx-users] Protein-ligand - genion error

Hi Justin, Thank you for your response. The co-ordinate file that you have mentioned. Is it the one obtained after running pdb2gmx step or the one after running genbox step? Also, I am putting few outputs for your referral.. My co-ordinate file after building topology and incorporating my

Re: [gmx-users] Protein-ligand - genion error

On 8/10/12 1:26 PM, Ankita naithani wrote: Hi Justin, Thank you for your response. The co-ordinate file that you have mentioned. Is it the one obtained after running pdb2gmx step or the one after running genbox step? Also, I am putting few outputs for your referral.. My co-ordinate file

Re: [gmx-users] Protein-ligand - genion error

Hi Justin, Thank you so much for your reply. It really helped me a lot. I think I have managed to clear this step. Thanks once again. Best Wishes, On Fri, Aug 10, 2012 at 6:30 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/10/12 1:26 PM, Ankita naithani wrote: Hi Justin, Thank you for

Re: [gmx-users] a residue move in extremely large scale in MD

Dear Dr. Dallas Warren, My protein is a protein-peptide complex. The residues I mentioned which moves in a large scope is from the peptide, it is the last 3rd residue of the peptide, a lysine. I compared this lysine position with the other residue positions (including the peptide binding

Re: [gmx-users] a residue move in extremely large scale in MD

On 8/10/12 7:58 PM, Acoot Brett wrote: Dear Dr. Dallas Warren, My protein is a protein-peptide complex. The residues I mentioned which moves in a large scope is from the peptide, it is the last 3rd residue of the peptide, a lysine. I compared this lysine position with the other residue

Re: [gmx-users] a residue move in extremely large scale in MD

Dear Justin,   Can you explain to me what do you mean for trjconv -pbc mol -ur compact followed by trjconv -center. Does it mean 2 steps command, with the first step as trjconv -pbc mol -ur compact and the second step as trjconv -center? Or can we merge it as a single step step? Second, will

Re: [gmx-users] a residue move in extremely large scale in MD

On 8/10/12 8:19 PM, Acoot Brett wrote: Dear Justin, Can you explain to me what do you mean for trjconv -pbc mol -ur compact followed by trjconv -center. Does it mean 2 steps command, with the first step as trjconv -pbc mol -ur compact and the second step as trjconv -center? Or can we merge

Re: [gmx-users] a residue move in extremely large scale in MD

you have to submit 10X with different seed simulation to confirm your results. 10ns is not converged for some simulation, you should also extend it in nowadays timescale level. Moreover, if you don't have biochemistry data to support your idea, nobody will believe your results. good luck