[gmx-users] (no subject)

http://kriture.com/site/wp-admin/images.php?time157.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!

[gmx-users] rotamers and rings

stereochemistry of the molecule after the minimisation. Is this possible? Sorry for bothering you again and thank you in advance for your help,Abdullah Ahmed -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] rotamers during minimization

I have been unable to induce gromacs to do this on its own during minimization. I could of course, change the original structure but I prefer not to. Thank you in advance, Abdullah Ahmed My .mdp file is as follows: ;; User spoel (236); Wed Nov 3 17:12:44 1993; Input file;;cpp

[gmx-users] Increasing machine precision

Hello, Is there a way to continue minimizing after reaching machine precision? Emtol and the number of iterations are sufficient to continue. I am assuming that reaching machine precision means that the gradient of change from one iteration to another has become so small that further minimizat

[gmx-users] Minimization and torsion angles

Hello, I have an input structure with poor torsion angles and after minimization with gromacs (both steepest descent and congugate gradient) I found that they were not corrected. There is enough free space for the torsion angles to be corrected. (I am sure of this because when I run the same

[gmx-users] minimization quagmire

Hello everyone, I have a question regarding the results of minimization. I have two structures that are the same except for 2 residues in the core of the structure that have been changed from luecine to to glycine. The leucine structure is very well packed and the core is hydrophobic. The in

[gmx-users] Internal Density

Dear all, I have 2 structures similar to a Beta-turn where the inside is hydrophobic, and I would like to find the density of just this part of the strucuture. More specifically, both structure are identical expect for one mutation. One of the structures contains 2 glycines facing each other

[gmx-users] editconf

Hello, I'd like to ask a question about the conversion of the results of minimization to pdb format. Here is what I do: Apply pdb2gmx to the pdb file to convert it to .gro and .top (pdb2gmx -f -p -o)Run editconf to define the box (editconf -d 1)run gromp and mdrun for the minimizationRun e

RE: [gmx-users] position restraints

and why. Thank you again for your help, Abdullah > Date: Thu, 3 Jun 2010 09:43:18 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] position restraints > > > > abdullah ahmed wrote: > > Hi! > > > > In your previous

FW: [gmx-users] position restraints

Hi! In your previous mail you mentioned: The position restraints must belong to the [moleculetype] of the species to be restrained. Once you #include a new molecule, you start a new [moleculetype] entry and the position restraints belong to it. So I rechecked my .top file and found th

FW: [gmx-users] position restraints

0 1000 ; 4 1 1000 0 1000 ; 5 1 1000 0 1000 ; 6 1 1000 0 1000 ; 7 1 1000 0 1000 ; 8 1 1000 0 1000 ; 9 1 1000 0 1000 ; > Date: Thu, 3 Jun 2010 09:00:36 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] position restraints > > > &g

[gmx-users] position restraints

Hello, I would like to restrain my molecule to a specific position in space. I would like for certain atoms to lie on the y-axis. To do this I used the following code/lines in my .top file: [ position restraints ] 2 1 1000 0 1000 ; 3 1 1000 0 1000 ; 4 1 1000 0 1000 ; 5 1 1000 0 1000 ; 6 1

[gmx-users] The components on potential energy

Hello, I would like to ask for some information about the potential energy term in the log file after minimization. I have used the OPLS-AA forcefield to conduct minimization. I understand that it is the addition of a group of energy terms (bond energy, angle, LJ ect..) however, I do not kno

[gmx-users] electro-static interaction not made

Dear GROMACS users, I have a protein structure with two oppositely charged residues facing each other. They are close enough for an electrostatic interaction to occur between them. However, this does not occur. After minimization they are in the exact same positions as before. Is there some

RE: [gmx-users] naive question about the c-terminus

jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] naive question about the c-terminus > > > > abdullah ahmed wrote: > > I'm sorry I should have been more clear. Because the PDB file starts > > from residue number 23, the residue labelled 4

RE: [gmx-users] naive question about the c-terminus

-0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] naive question about the c-terminus > > > > abdullah ahmed wrote: > > I'm sorry I should have been more clear. Because the PDB file starts > > from residue number 23, the resi

RE: [gmx-users] naive question about the c-terminus

naive question about the c-terminus > > > > abdullah ahmed wrote: > > Hello everyone! > > > > I have a naive question and I have been trying to find a solution > > myself, but I just don't understand what is wrong. > > > > When I run pdb2

[gmx-users] naive question about the c-terminus

Hello everyone! I have a naive question and I have been trying to find a solution myself, but I just don't understand what is wrong. When I run pdb2gmx with "-ter" on my molecule I get the following error message when I ask for a COOH to be made at the C terminus (I get no error when I ask

[gmx-users] distances between atoms in an electrostatic interaction

Dear Gromacs users, I have an electrostatic interaction in my structure between GLU and LYS. After minimization the distance between the Hydrogen molecule on the Lysine and the Oxygen on the GLU is reduced to 1.4 A°. Is it possible to pre-set this distance to be 1.6 A° instead? I realize t

RE: [gmx-users] electro-static potential energy after minimization

t the editconf/genbox stage. Is there another way to do this? Thanks again, and Bonne Journée! Abdullah > Date: Wed, 5 May 2010 01:47:29 +1000 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] electro-static potential energy after minimiza

re: [gmx-users] electro-static potential energy after minimization

omacs.org > Subject: Re: [gmx-users] electro-static potential energy after minimization > > > > abdullah ahmed wrote: > > Thank you for your reply, > > > > However, I can not use MD. > > I would simply like to ask whether I am correct in assuming that the >

RE: [gmx-users] electro-static potential energy after minimization

> Subject: Re: [gmx-users] electro-static potential energy after minimization > > > > abdullah ahmed wrote: > > Hello everyone, > > > > I have two protein structures, and the insides of both are not exposed > > to water. > > One structure contains two

[gmx-users] electro-static potential energy after minimization

if providing PDB and .mdp files would be helpful, but I can send then in my next mail if neccesary. Thank you in advance! Abdullah Ahmed _ Your E-mail and More On-the-Go. Get Windows Live

RE: [gmx-users] electrostatic interactions

I wish I could use a picture :) Unfortunately, this is not possible since I need the energy value to be able to compare this to other mutations of the same structure and to provide a "measure" of how energetically favourable one is in comparison to the other. And I am using a box of water becau

RE: [gmx-users] electrostatic interactions

Actually I'd just like to know why both structures have such similar coloumb energy values. If an electro-static interaction is being made in one structure and not in the other then their coloumb energy values should be different too, no? Wouldn't this be visible with simple energy minimisatio

RE: [gmx-users] electrostatic interactions

ometry is identical with the exception of the second charged residue, which is replaced by Leucine in one structure. > Date: Mon, 3 May 2010 12:11:12 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] electrostatic interactions > > &g

RE: [gmx-users] Unneccessary bonding

face of the protein > may be a missing water molecule in between them? > > > > -Justin > > > >> Abdullah > >> > >> From: x.peri...@rug.nl > >> To: gmx-users@gromacs.org > >> Subject: Re: [gmx-users] Unneccessary bo

RE: [gmx-users] Unneccessary bonding

, abdullah ahmed wrote:Thank you very much for your reply, I agree it is probably a visualization of the effect, and that there is no bond. However, the distance between the two atoms participating in this "phantom bond" is 1.4 A°. Isn't that too close? Shouldn't it be considered a

[gmx-users] electrostatic interactions

, the results show that they are almost the same. Thank you in advance for your help, Abdullah Ahmed _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup

RE: [gmx-users] Unneccessary bonding

llah From: x.peri...@rug.nl To: gmx-users@gromacs.org Subject: Re: [gmx-users] Unneccessary bonding Date: Mon, 3 May 2010 17:36:29 +0200 On May 3, 2010, at 5:16 PM, abdullah ahmed wrote:Hello, I am a new user to GROMACS and so this question maybe somewhat naive. My objective is t

[gmx-users] Unneccessary bonding

at the log-file). However, a covalent bond is being created between them instead. This should not be happening. Does anyone have any ideas on what may be happening and how I can fix it? If this information is not sufficient, please let me know, and thank you in advance. Abdu