[gmx-users] Freezing group

Hi dear All! Good day dear forum! I have a question abour freezing of atoms during MD. The idea is that - I have a protein and one domain contains a site. Also I have two ligands, one of them is better inhibitor in comparison with another one. To prepare the topology of the inhibitor I need to use

[gmx-users] Implicit solvent

Hi, dear developers! I want to ask you abou dynamics in implicit solvent. I have a complex of animal protein - dimer/trimer. After modeling by homology I have built another one from the plant organism. Dimer/trimer was constructed with superposition method. The question is - can I use imlicit solv

[gmx-users] repost_hybrid imlicit/explicit solvent

Hi this is a repost, maybe it was missed. I want to create a system with hybrid solvent (explicit/implicit). My system is large enough to calculate it with explicit SOL. But it is critical to study the behavior of several water molecules in the site. The idea is to generate a layer of explicit wat

[gmx-users] hybrid solvent model

Hi all. I want to create a system with hybrid solvent (explicit/implicit). My system is large enough to calculate it with explicit SOL. But it is critical to study the behavior of several water molecules in the site. The idea is to generate a layer of explicit water molecules around the protein mo

[gmx-users] Phosphorylation

Hi, all. Does anybody know wether I have to put a phosphorylated residue in the kinase's activation loop (last example is pdbid 2Y94) or not, when I'm working with protein-inhibitor complex without any type of protein-protein interactions? Or it is necessary only when I'm working with p-p complexes

[gmx-users] amber-lipid

Hi Is it possible to use amber forcefield with lipid parameters like it was done with gmx in "KALP-15 in DPPC" tutorial? I have to use amber forcefield as it is neccessary for parametrization of my ligand and its stecking interactions. Thank you very much -- Nemo me impune lacessit -- gmx-us

[gmx-users] several itp

Hi all. Justin, thank you for you quick respons ))) I want to clarify a situation with a number of ligands I can use in one simulation. I have got files of 3 ligands converted from amber files to gromacs with amb2gmx.pl script. To include this files in the topology file I changed the extension of t

[gmx-users] pull_distance

hi all. I need your advice. I have marked several atoms from one chain and several atoms from another chain (about 8 from each chain), they are forming 5 h-bonding places, and now I want to stabilize the distance between this chains during the MD. Can I use com pulling distance Y Y Y for it with

[gmx-users] ATP+Mg

Hi all. I need your advices about my task which is closely associated with ATP toplogy in the binding site. As I understood from one of the letters ( http://archive.ambermd.org/201106/0522.html) I can use antechamber or derive charges from the site linked in the letter. But the ATP's phosphate tail

[gmx-users] MD duration

Hi all. I want to ask you a question about the length of dynamics. Is it enough to set time at 3-5ns to see the motion and affinity of the ligand (nucleotide derivate) the protein's domain size is nearly 200 aminoacids. The protein was optimized earlier. Moreover, is it enough for drug design scre

[gmx-users] Re: gmx-users Digest, Vol 90, Issue 82

on of the residues in the peptide is acylation. But may be you know something! Thank you very much? On 17/10/2011 5:01 PM, Алексей Раевский wrote: > Hi! > I need an advice concerninng topology building of such substance like > cyclosporine A. I've tried to make it with antech

[gmx-users] cyclosporine A

Hi! I need an advice concerninng topology building of such substance like cyclosporine A. I've tried to make it with antechamber tool, cause I wanted to use amber99sb forcefield. But the program gave me an error in the begining and no results in the end after 12 hours of calculations ))) Can you gi

[gmx-users] angke definition

Hi, i need your help again! this time in the selection of analyzing tools and methods... I've found a water molecule near one of the ligand atoms. It's stabile enough and the distance is about 3.3 A. But I want to make some measurments, exactly angle degree identification. I want to calculate the f

[gmx-users] Re: gmx-users Digest, Vol 89, Issue 52

ML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110910/3611a8e9/attachment-0001.html > > -- > > Message: 5 > Date: Fri, 09 Sep 2011 17:02:40 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-us

[gmx-users] (no subject)

Hi. I've look through the manual and didn't find an answer on my question: i've got a trajectory and i want to convert it in *.pdb with such parameters of index file [all atoms within a sphere with a chosen radius around selected atom]. What can i do? Thank you -- *С уважением! *** * Nemo me

[gmx-users] mdp params and forcefields

Hi. I need your help dealing with parametrization of mdp file. Look, I want to understand how can we change such params like rlist, rvdw, cut-off, rcoulomb. As I know each forcefield has its own properties and calculated values of this params. But I've found that in different articles this values w

[gmx-users] Re: gmx-users Digest, Vol 83, Issue 130

> > Hi! > > I'm working with kinase with ATP in active site. ATP topology was > > created by swissparam.ch server, as well as I'm > > working with charmm27 in gromacs 4.5.3. Using superposition of the > > protein models I've found coordinates for ions which have to stabilize

[gmx-users] ATP+Mg

Hi! I'm working with kinase with ATP in active site. ATP topology was created by swissparam.ch server, as well as I'm working with charmm27 in gromacs 4.5.3. Using superposition of the protein models I've found coordinates for ions which have to stabilize ATP (Mg2+). For this purpose we used MgCl

[gmx-users] (no subject)

Hi, I have got a situation and I don't know how to cope with it. I carried out a simulation in gromacs 4.5.3 and the objects are protein, rna, water...The idea is that one atom part of rna has to create an h-bond with a water molecule, which at the same time makes h-bonds with aminoacids of the bin

[gmx-users] trjconv problem

Hi, I want to ask you for help. I've got a trr file after 5 ns simulation on the desktop 2 quad. The object is a complex of protein and ligand (the itp file for ligand was prepeared by server), in adition, I made some changes in rtp, atp, bon.itp databases to obtain a phosphorylated tyrosine. When

[gmx-users] include a few .itp files

Hi. I have some problems using ff_charmm27 ported in gromacs 4.5.3. 1) I want to build a topology of phosphorylated tyrosine in one position of activated protein. I can make it with swissparam.ch server (getting .itp) or by my hands. But the situation is complicated enough for me, because of necess

[gmx-users] Reducing distance between atoms! PULL

Sorry, I want to ask the same question I had a week ago. I need your advice in COM PULL. This is a part of article which describes methodology "...with respect to the atomic distance between the carbonyl carbon of the substrate and the oxygen atom of the identified nucleophilic water, a constraine

[gmx-users] Pulling water

Sorry, I want to ask the same question I had a week ago. I need your advice in COM PULL. This is a part of article which describes methodology "...with respect to the atomic distance between the carbonyl carbon of the substrate and the oxygen atom of the identified nucleophilic water, a constraine

[gmx-users] COM Pulling

Hi all ! I have a results of my MD and i have found a water molecule that was getting closer to my substrate on one frame of my dynamic. The distance is 3.4 A. Now I have to immobillize this water on this distance during the next step of MD by using a harmonic potential as the distance constraint,

[gmx-users] 2 questions

Hi all. I'm working with gromacs 4.0.5 in amber99 force field. I have two questions: 1. The protein part of my complex (trna+protein) consists of 870 aminoacids and two atoms of Zn. The question is - whether I have to create an index file, which will unit aminoacids and Zn in one "protein" or not

[gmx-users] Re: gmx-users Digest, Vol 67, Issue 89

Sorry for so disordered questions... <3. use the pull code. I don't know exactly what you want to do here...perhaps harmonically restrain the distance between the two mentioned groups to some specified value? No need to rename the water, just make an index group.> The problem is that I don't know

[gmx-users] PULLING

Sorry for so disordered questions... <3. use the pull code. I don't know exactly what you want to do here...perhaps harmonically restrain the distance between the two mentioned groups to some specified value? No need to rename the water, just make an index group.> The problem is that I don't know

[gmx-users] PULLING

Sorry for so disordered questions... <3. use the pull code. I don't know exactly what you want to do here...perhaps harmonically restrain the distance between the two mentioned groups to some specified value? No need to rename the water, just make an index group.> The problem is that I don't know

[gmx-users] PULLING

Hi all. I have to reproduce an experiment from the article "Identification of the nucleophilic factors and the productive complex for the editing reaction by leucyl-tRNA synthetase" (by Yohsuke Hagiwara a,b, Osamu Nureki c, Masaru Tateno a,b,*). This is one of the steps of education I have to comp