Re: [gmx-users] RMSIP

- Original Message - From: pawan raghav Date: Wednesday, May 19, 2010 16:28 Subject: [gmx-users] RMSIP To: gmx-users@gromacs.org > Thanks mark, but I think that g_anaeig calculates the degree of overlap then > what method would you use to calculate this?> I don't know what you are as

[gmx-users] Re: OPLS-AA/L force field

Hi Justin, Thank you for your help, But when I run x2top command there is one error that is:"Can not find forcefield for atom C1-1 with 2 bondsCan not find forcefield for atom C4-4 with 2 bonds...Program x2top, VERSION 4.0.5Source code file: x2top.c, line: 207Fatal error:Could only find a force

Re: [gmx-users] water medium

but genion only accepts one type of ion, how can we insert different types? On Tue, May 18, 2010 at 3:38 PM, Justin A. Lemkul wrote: > > > tahereh tekieh wrote: > >> dear friends >> i want to simulate a water medium in which 5 types of different ions flow >> in it. how can i do that with gromacs

Re: [gmx-users] water medium

- Original Message - From: tahereh tekieh Date: Wednesday, May 19, 2010 17:09 Subject: Re: [gmx-users] water medium To: jalem...@vt.edu, Discussion list for GROMACS users > but genion only accepts one type of ion, how can we insert different types? I suggested some approaches to this

Re: [gmx-users] DSSP

Hi, there was a problem in do_dssp when used on proteins with more than 10 chains. Is this the case? I just saw that I only fixed that in the head, but not in 4.0.x. Carsten On May 18, 2010, at 3:49 PM, shahid nayeem wrote: > Hi > When I run dssp alone with a .pdb file it works well. But w

Re: [gmx-users] RMSIP

Hi, The answer is given by g_anaeig (-h): When -v, -eig, -v2 and -eig2 are given, a single number for the overlap between the covariance matrices is generated. The formulas are: difference = sqrt(tr((sqrt(M1) - sqrt(M2))^2)) normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2)) s

[gmx-users] Re: water medium

the list. Use the www interface > > or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-user

Re: [gmx-users] Re: water medium

Pages/Personal/justin > > > > > > > > > -- > > > gmx-users mailing listgmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://ww

[gmx-users] Solvation free energy

Hi, I want to calculate the solvation free energy of Wild-type human IAPP (hIAPP) with 37 residues in length that residu26 isoleucine is mutated to proline (ile26pro). I used dual topology in Thermodynamic integration (TI) for calculating salvation free energy. For the solvation free energy calcu

Re: [gmx-users] Re: water medium

lman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the www interface > > or send it to gmx-users-requ...@gromacs.org <mailto:gmx-user

Re: [gmx-users] Re: OPLS-AA/L force field

you zou wrote: Hi Justin, Thank you for your help, But when I run x2top command there is one error that is: " Can not find forcefield for atom C1-1 with 2 bonds Can not find forcefield for atom C4-4 with 2 bonds ... Program x2top, VERSION 4.0.5 Source code file: x2top.c, line: 207 Fatal err

[gmx-users] enegry minimisation

Hello All This question may sound trivial to many, but as i am new to this field, please help. I want to ask a question regarding my previous query of distortion of protein strucutre after molecular dynamcs simulation. I have noticed that after enegry minimisation using steepest decent algorithm,

Re: [gmx-users] Re: OPLS-AA/L force field

Can you not run pdb2gmx for each of your molecules that you want separate force fields for? Then cat the gro files, renumber and include the molecule types as .itp files in the .top file as below. If I'm doing anything wrong please let me know! :) ; ;This is your topology file ;"What If N

Re: [gmx-users] enegry minimisation

sonali dhindwal wrote: Hello All This question may sound trivial to many, but as i am new to this field, please help. I want to ask a question regarding my previous query of distortion of protein strucutre after molecular dynamcs simulation. Can you provide a link to your previous post, for

Re: [gmx-users] enegry minimisation

sonali dhindwal skrev: Hello All This question may sound trivial to many, but as i am new to this field, please help. I want to ask a question regarding my previous query of distortion of protein strucutre after molecular dynamcs simulation. I have noticed that after enegry minimisation using s

Re: [gmx-users] Re: OPLS-AA/L force field

Oliver Grant wrote: Can you not run pdb2gmx for each of your molecules that you want separate force fields for? Then cat the gro files, renumber and include the molecule types as .itp files in the .top file as below. If I'm doing anything wrong please let me know! :) Combining different for

[gmx-users] enegry minimisation

Hello All This question may sound trivial to many, but as i am new to this field, please help. I want to ask a question regarding my previous query of distortion of protein strucutre after molecular dynamcs simulation. I have noticed that after enegry minimisation using steepest decent algorithm,

Re: [gmx-users] enegry minimisation

sonali dhindwal skrev: Hello All This question may sound trivial to many, but as i am new to this field, please help. I want to ask a question regarding my previous query of distortion of protein strucutre after molecular dynamcs simulation. I have noticed that after enegry minimisation using s

Re: [gmx-users] enegry minimisation

Thanks Justin for your reply. Yes I have included solvent in the protein using genbox. I am pasting .mdp file which I used for MD simulation : title   = trp_drg MD cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator  = md dt   

Re: [gmx-users] enegry minimisation

sonali dhindwal wrote: Thanks Justin for your reply. Yes I have included solvent in the protein using genbox. Then you should do energy minimization after constructing the system. I am pasting .mdp file which I used for MD simulation : title = trp_drg MD cpp =

Re: [gmx-users] enegry minimisation

Sorry, but I couldnt get your question, I have used this .mdp file for energy minimisation after addition of water and using GROMOS96 43a1 force field : title    = drg_trp cpp  = /lib/cpp ; location of cpp on SGI define   = -DFLEX_SPC ; Use Ferguson’s Flexible water mod

Re: [gmx-users] enegry minimisation

After adding water you can do energy minimization (EM) in two steps: 1. Constrain the protein backbone and do EM. 2. Now do EM on the full system. 3. Run a short MD simulation by constraining the protein backbone. The above three steps will help hydrate the protein molecule with minimal distortion

Re: [gmx-users] enegry minimisation

Gaurav Goel wrote: After adding water you can do energy minimization (EM) in two steps: 1. Constrain the protein backbone and do EM. 2. Now do EM on the full system. 3. Run a short MD simulation by constraining the protein backbone. The above three steps will help hydrate the protein molecule

[gmx-users] g_cluster, RMSD distribution

Dear All I’m trying to obtain RMSD distribution of a ligand in the binding site of the receptor protein during 40 ns MD simulation. Could you please explain: - what is exactly the yaxis unit of the plot obtained using g_cluster with –dist option - how is this distribution calculated? Thank

Re: [gmx-users] enegry minimisation

On Wed, May 19, 2010 at 9:18 AM, Justin A. Lemkul wrote: > > > Gaurav Goel wrote: >> >> After adding water you can do energy minimization (EM) in two steps: >> >> 1. Constrain the protein backbone and do EM. >> 2. Now do EM on the full system. >> 3. Run a short MD simulation by constraining the pr

[gmx-users] Re: Re: crystallographic water to tip4p model

>> Hi, >> I wanna keep crystallographic water with tip4p model for md simulation but when I use pdb2gmx even if I set "-water tip4p" it protonates oxygens to spc water model instead. >> Is there any way to replace spc water molecules with tip4p water molecules in the same orientation? > >What's you

Re: [gmx-users] enegry minimisation

Thanks Justin for your help I checked the mdout.mpd, all the parameters were interpereted correctly, though from next time i will take care of putting space. regarding you asked if those are small molecules, yes those are the ligands and i have taken .itp and .gro file from Dundee Prodrg server.

Re: [gmx-users] enegry minimisation

sonali dhindwal wrote: Thanks Justin for your help I checked the mdout.mpd, all the parameters were interpereted correctly, though from next time i will take care of putting space. regarding you asked if those are small molecules, yes those are the ligands and i have taken .itp and .gro file

[gmx-users] Phosphorylation of protein

gt; > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.ed

Re: [gmx-users] g_cluster, RMSD distribution

Hi, The distribution is calculated as follows: 101 bins are formed between zero and maximum rmsd in equal separation (by calculating the largest value by 100 to create the separation). Each rmsd value is put into the right bin and the counter for that bin is increased by 1. The total number of cou

[gmx-users] Re: OPLS-AA/L force field

Hi again, Sorry I confused you with my question. My question is How can I make .gro file and .top file from drug.pdb (that removed from drug-enzyme.pdb)? If I can use x2top command I will make .top file just, is it true? I think .gro file is dependent on forcefiled too so If I use editconf com

[gmx-users] energy decreasing in NVE simulation

Dear all, When I try to simulation with NVE ensemble, the total energy keeps decreasing. Geometry optimization and solvent equilibration are done before the NVE simulation. I follow the requirements provided in http://www.gromacs.org/Documentation/Terminology/NVE Would any one help me to figur

[gmx-users] acetonitrile from amber to gromacs

hi all together, this week i'm trying to do some simulations with acetonitrile (AN) as a solvent and using ffamber99 as force field. on this website http://www.pharmacy.manchester.ac.uk/bryce/amber#box i found a gorgeous little box containing a pretty number of 6-site modeled AN molecules, repr

Re: [gmx-users] acetonitrile from amber to gromacs

Hi, You could use acpype, although you will need to push more than one button :-) http://code.google.com/p/acpype/ Cheers, Rui Rodrigues On Wed, 19 May 2010 18:15:29 +0200, vedat durmaz wrote > hi all together, > > this week i'm trying to do some simulations with acetonitrile (AN) as a > solve

Re: [gmx-users] Re: OPLS-AA/L force field

you zou wrote: Hi again, Sorry I confused you with my question. My question is How can I make .gro file and .top file from drug.pdb (that removed from drug-enzyme.pdb)? If I can use x2top command I will make .top file just, is it true? I think .gro file is dependent on forcefiled too so If I

[gmx-users] Re: acetonitrile from amber to gromacs

> > hi all together, > > this week i'm trying to do some simulations with acetonitrile (AN) as a > solvent and using ffamber99 as force field. on this website > > http://www.pharmacy.manchester.ac.uk/bryce/amber#box > > i found a gorgeous little box containing a pretty number of 6-site > modeled AN

[gmx-users] Constraint distance question

Hi, I am trying to look at the free energy differences as a function of end-to-end distance of peptides in water. I am running a set of simulations with the two atoms of interest joined by a type 2 constraint, with the length varying from 0.5 to 3 nm. However, these simulations all ex

Re: [gmx-users] acetonitrile from amber to gromacs

I did it for other solvent. If you have AMBER is very easy to do. Do you have AMBER? On Wed, May 19, 2010 at 12:15 PM, vedat durmaz wrote: > > hi all together, > > this week i'm trying to do some simulations with acetonitrile (AN) as a > solvent and using ffamber99 as force field. on this website

Re: [gmx-users] acetonitrile from amber to gromacs

thanks to all so far @anthony i have amberTools, but not the amber MD package. is that enough for my purpose? @rui acpypi -i ch3cn_210.pdb says: "cannot find template for residue C3N in our library". and indeed, there's no residue C3N in my ffamber99sb.rtp file (and i don't know, how to use it

[gmx-users] weird problem about editconf and genbox

Hi, I have two questions concerning generating a solvent box for my protein using gromacs 3.3.1. 1) I used to use editconf to generate a dodecahedron box, then use genbox. It used to work fine: $editconf -f protein.gro -o protein_box.gro -d 0.9 -bt dodecahedron -c $genbox -cp protein_box.gro -c

Re: [gmx-users] weird problem about editconf and genbox

Lin Xu wrote: Hi, I have two questions concerning generating a solvent box for my protein using gromacs 3.3.1. Any particular reason you're using software that is over four years old? Gromacs 4.0.7 will give you a major speed upgrade, and lots of new features. 1) I used to use editconf t

[gmx-users] confusion about segmentation fault during mdrun

Hi All, I understand that the error of segmentation fault may come from many reasons, but I just couldn't figure out the reason of this error in my simulations. I want to run md simulations with explicit water for 20 structures of one domain (residue 77-148) of calmodulin (PDB 1CFC). These

Re: [gmx-users] energy decreasing in NVE simulation

For more exotic NVE-systems I had to do some or several of the following things to get stable Etot: * have an even shorter timestep than one would expect from the applied constraints and such. * use double precision. * apply the constraints with lower tolerance/more iterations etc. Then there's

Re: [gmx-users] confusion about segmentation fault during mdrun

Lan Hua wrote: Hi All, I understand that the error of segmentation fault may come from many reasons, but I just couldn't figure out the reason of this error in my simulations. I want to run md simulations with explicit water for 20 structures of one domain (residue 77-148) of calmodu

[gmx-users] Re: acetonitrile from amber to gromacs

Dear Vedat, On Wed, May 19, 2010 at 20:36, wrote: > @rui > acpypi -i ch3cn_210.pdb > says: "cannot find template for residue C3N in our library". and indeed, > there's no residue C3N in my ffamber99sb.rtp file > > (and i don't know, how to use it in order to generate my topology or even > an rtp

[gmx-users] energy break down

Hello, I am trying to get only interaction energies (vdw and electrostatics) between hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in the system. I have added *exclusions section* at the end of top file to exclude all nonbonded interactions between atom 1 and all other 20 atoms.

Re: [gmx-users] confusion about segmentation fault during mdrun

Hi Justin, Thank you so much for your quick reply and good suggestions. The following is my answer. On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul wrote: > > > Lan Hua wrote: > >> Hi All, >> >> I understand that the error of segmentation fault may come from many >> reasons, but I ju

Re: [gmx-users] energy break down

Moeed wrote: Hello, I am trying to get only interaction energies (vdw and electrostatics) between hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in the system. I have added _exclusions section_ at the end of top file to exclude all nonbonded interactions between atom 1 and

Re: [gmx-users] confusion about segmentation fault during mdrun

Lan Hua wrote: Hi Justin, Thank you so much for your quick reply and good suggestions. The following is my answer. On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul > wrote: Lan Hua wrote: Hi All, I understand that the error of segm

RE: [gmx-users] enegry minimisation

> I seem to say this several times per week: in my experience (and in the > experience of many others who have posted here) the charges and charge > groups output by PRODRG are often unsatisfactory, requiring manual Might be an idea then to put the comments on the PRODRG page on the GROMACS websit

Re: [gmx-users] enegry minimisation

Dallas B. Warren wrote: I seem to say this several times per week: in my experience (and in the experience of many others who have posted here) the charges and charge groups output by PRODRG are often unsatisfactory, requiring manual Might be an idea then to put the comments on the PRODRG p

Re: [gmx-users] confusion about segmentation fault during mdrun

Hi Justin, I appreciated your quick answers. So if I understand correctly, using constraints = hbonds with the time step of 2fs, it should be fine, right? Thanks, Lan On Wed, May 19, 2010 at 3:52 PM, Justin A. Lemkul wrote: > > > Lan Hua wrote: > >> Hi Justin, >> >> Thank you so much for

Re: [gmx-users] confusion about segmentation fault during mdrun

Lan Hua wrote: Hi Justin, I appreciated your quick answers. So if I understand correctly, using constraints = hbonds with the time step of 2fs, it should be fine, right? Maybe. If your goal is REMD (I'm not clear from your original post) then stability may be an issue at higher tem

Re: [gmx-users] confusion about segmentation fault during mdrun

Thanks. The simulations are regular MD in explicit water at room temperature. Lan On Wed, May 19, 2010 at 6:03 PM, Justin A. Lemkul wrote: > > > Lan Hua wrote: > >> Hi Justin, >> >> I appreciated your quick answers. So if I understand correctly, using >> constraints = hbonds with the time

[gmx-users] Re: [gmx-user]Error by pdb2gmx (Mark Abraham)

Dear Mark: I used gromacs version 3.3.1. I update ffG45a3.rtp to include my molecule. And the rtp of my molecule is in the attached file DRG.txt.   Thank you very much!   Angel [ DRG2 ] [ atoms ] CCN CH3 0.0 1 CCM CH1 0.08300 2 CCO CH3 0.03300 2

[gmx-users] breaking down total energy

Hello Justin, Thanks for your comments. Actually, since I am interested in only interaction energies *between* molecules I thought by excluding energies between atoms on a single chain what I get from nonbonded interactions would not include 1-4 interactions. *

[gmx-users] g_clustsize output

Hello, I have a system of dimers which spontaneously assemble into clusters. I would like to get a plot of the number of clusters of size s vs s. In looking at g_clustsize I am able to obtain the average number of clusters vs time, the average cluster size vs time and a histogram of the ave

Re: [gmx-users] g_clustsize output

On 2010-05-20 04.55, toma0...@umn.edu wrote: Hello, I have a system of dimers which spontaneously assemble into clusters. I would like to get a plot of the number of clusters of size s vs s. In looking at g_clustsize I am able to obtain the average number of clusters vs time, the average cluster

[gmx-users] Charge assignment

Hi everyone.   I'm working on getting parameters for a protein system that has some linker residues in it.  These linkers are nothing too strange, they just have some amine groups.  I can get bonded parameters from the prodrg server.  I know the charge groups are unreliable.  I'm using the 53A6