[gmx-users] Cytochrom C

Hi all, Has anybody made initial configuration for Cytochrom C? Can it be shared with me? Thanks, Dariush -- 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 befor

Re: [gmx-users] Cytochrom C

heir website; I used martinize.py script; Again I got error. Regards, Dariush On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkul wrote: > > > Dariush Mohammadyani wrote: > >> >> Hi all, >> >> Has anybody made initial configuration for Cytochrom C? Can it be

Re: [gmx-users] RDF(PMF) and Umbrella sampling

e umbrella mdp files. > >>>> > >>>> pull= umbrella > >>>> pull_geometry = distance > >>>> pull_dim = Y Y Y > >>>> pull_start = no > >>>> pull_ngroups = 1 > >>>> pull_group0 = cage

Re: [gmx-users] Cytochrom C

t; bob h. > > > > > On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote: > > Yes, I have PDB file (1HRC.pdb). However, when I try to use "pdb2gmx" I > get this error: > > Residue 'HEM' not found in residue topology database > > and HEM is Iron

Re: [gmx-users] Cytochrom C

gt; > > OO -0.515 > > >[ bonds ] > > > CH3HH31 > > > CH3HH32 > > > CH3HH33 > > > CH3C > > > C O > > > > > > Surprisingly, an .hdb entry for

Re: [gmx-users] umbrella sampling tutorial quastion

(un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh Sch

Re: [gmx-users] Cytochrom C

Does anybody know where can I find [ HIS ] parameters? Thanks, Dariush On Sat, Jan 7, 2012 at 3:58 AM, Dariush Mohammadyani < d.mohammady...@gmail.com> wrote: > Dear Peter and Krzyszto, > > Thank you. I am following your comments. If I get any problem I will come > back. >

Re: [gmx-users] Cytochrom C

Dear Justin, I could not find HIS in CHARMM and GROMOS53a6. Somebodies offer to rename it to HSE or HSD, but I do not know why? and which one is correct. I am working on Cytochorom c. Thanks, Dariush On Tue, Jan 10, 2012 at 4:22 PM, Justin A. Lemkul wrote: > > > Dariush Mohammady

[gmx-users] Coarse Grained Cytochrom C

Hi all, Has anybody used Coarse grained model for Cytochrome C? I could create a model using MARTINI forcefiels (using martinize.py script and 1HRC.pdb file), but it does not have HEM and HOH groups. Can anybody help me? Kind Regards, Dariush Mohammadyani Department of Structural Biology

Re: [gmx-users] Cytochrom C

g 'HIS' names and interactive setup is that bonds to > heme > iron will be generated based on the 'specbond.dat' entries, if HIS NE2 > nitrogens are close enough to the FE. > > Krzysztof > > > > On 1/10/12 2:40 PM, Dariush Mohammadyani wrote: >

Re: [gmx-users] Cytochrom C

GROMACS 4.5.3 and charmm27.ff. Cytochrome C is a difficult protein to simulate :( Thanks, Dariush On Tue, Jan 17, 2012 at 10:33 AM, Justin A. Lemkul wrote: > > > Dariush Mohammadyani wrote: > >> According your help and "pdb2gmx -his -missing" I could create input

[gmx-users] NAMD file (.inp) convert to GROMACS format

Hi all, I have two files (Topology and Parameter files) in NAMD format (*.inp). I am going to use them in GROMACS. Can you help me how can I use them? Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501

Re: [gmx-users] NAMD file (.inp) convert to GROMACS format

Is there any similar script to change it for this reason? On Fri, Jan 27, 2012 at 11:26 AM, Justin A. Lemkul wrote: > > > Dariush Mohammadyani wrote: > >> Hi all, >> >> I have two files (Topology and Parameter files) in NAMD format (*.inp). I >> am going to

Re: [gmx-users] NAMD file (.inp) convert to GROMACS format

Thanks Justin! There is one script in User Contributions page, but it does not work. I totally changed my way, I will use NAMD in this case... On Fri, Jan 27, 2012 at 2:11 PM, Justin A. Lemkul wrote: > > > Dariush Mohammadyani wrote: > >> Is there any similar script to

Re: [gmx-users] Martini

SC5 does not work? Dariush -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA On Thu, Mar 8, 2012 at 2:34 PM, dina dusti wrote: > Dear Gromacs Speciali

Re: [gmx-users] Martini

-- > *From:* Dariush Mohammadyani > *To:* dina dusti ; Discussion list for GROMACS users > > *Sent:* Thursday, March 8, 2012 11:24 PM > *Subject:* Re: [gmx-users] Martini > > SC5 does not work? > Dariush > > -- > Kind Regards, > Dariush Mohammadyani

[gmx-users] clashes

figure it out? Or actually if we have some clashes in system how we can correct them? Thanks, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- gmx-users mailing list

Re: [gmx-users] clashes

ation"? Thanks, Dariush On Wed, Mar 14, 2012 at 10:08 AM, Justin A. Lemkul wrote: > > > Dariush Mohammadyani wrote: > >> Dear user, >> When I am using: >> genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro >> to add water in

Re: [gmx-users] Box Size in MD

As far as I concern, the minimum size is that cove all parts of your molecules or system. In case you should use solvent it is up to you to add how many molecules and in this case you should make decision by experience or according to literature. Dariush -- Kind Regards, Dariush Mohammadyani

Re: [gmx-users] About Distance.pl script

I have gotten this error previously. I changed the address of the g_dist (e.g. /user/gromacs/bin/g_dist) in distances.pl file and it works. Dariush On Thu, Mar 29, 2012 at 11:51 AM, vidhya sankar wrote: > Dear justin , Thank you for your previous reply > When i Download and run Distance.pl scri

[gmx-users] Position Restraints

Dear All, I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid bilayer. Although I used: define = -DPOSRES components in system were moving around and interact with each other. Then, I cannot do NVT or NPT equilibration. Could you please let me know how can I control thi

Re: [gmx-users] Position Restraints

: > > > On 4/26/12 1:35 PM, Dariush Mohammadyani wrote: > >> Dear All, >> I am using CG-MD using MARTINI forcefield. The system contains Protein >> and lipid >> bilayer. Although I used: >> define = -DPOSRES >> components in system were moving around and i

[gmx-users] fly some lipids to water

cardiolipin) fly away from bilayer and come inside the water. Does anybody know what is the problem? How should I fix my system? I am using Coarse grained model using MARTINI force field. Thanks, Dariush -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of

Re: [gmx-users] MARTINI parameters for dodecyl maltoside (DDM)

Have you checked MARTINI website? http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters Dariush Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA

Re: [gmx-users] MARTINI parameters for dodecyl maltoside (DDM)

ers for the polar head and the lipidic tail, so > it is worth trying to merge them > to have the correct representation! > > Francesco > > 2012/5/21 Dariush Mohammadyani > >> Have you checked MARTINI website? >> http://md.chem.rug.nl/cgmartini/index.

[gmx-users] Simple question (confout)

Hi, Is there any difference between confout.gro file and last frame which we can extract from trajectory? I am thinking they are different!! When I see the trajectory I can see the edge of the well-shaped box, but when I see confout.gro it is not well-shaped and some atoms looks went out out of th

[gmx-users] Bilayer curvature

Dear All, I have set two bilayers: 1. 400 DOPC 2. 320DOPC and 80 Cardiolipin Second one show significant curvature during NPT equilibrium and MD run (not in NVT eq.). Is it normal? For the first bilayer, after adding the protein to the system, here also I can see big curvature in the membrane. D