[gmx-users] Interaction energy

Dear all,     I have simulated a small peptide (+2 charge at pH=7) in water. Then i calculate the interaction energy using energy_grps = Protein SOL. The value of different energy terms are as follows:

[gmx-users] Selection of force fields

Dear Tsjerk,    Thanks for your reply. I am interested to work with ganglioside GM1. In that case which ffG will be appropriate for me. Ms. Anindita Gayen  C/O Dr. Chaitali Mukhopadhyay  Senior Research Fellow  Department of Chemistry  University of Calcutta  92, A. P. C. Road

[gmx-users] Dihedral definition

   func=3 for R.B. Is for proper dihedral 2nd 3rd atom and for improper dihedral 1st last atom is considered? Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Explore

[gmx-users] Selection of force field

(containing sugar moiety)? Looking forward for any reply. thanks in advance, Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Explore your hobbies and interests. Go to http

[gmx-users] (no subject)

installation run successfully. But when i run mdrun_mpi ..i got the message  Can't read MPIRUN_MPD and the mdrun_mpi program does not run. Any suggestion regarding this problem will be highly acceptable. thanks in advance, Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior

[gmx-users] gromacs in parallel version

successfully. But when i run mdrun_mpi ..i got the message  Can't read MPIRUN_MPD and the mdrun_mpi program does not run. Any suggestion regarding this problem will be highly acceptable. thanks in advance, Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow

[gmx-users] C-terminal amide capping

-terminal amide capping option is not incorporated. Can anyone please suggests me how i can achive this? Thanks in advance. Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Add

[gmx-users] P-N vector orientation

of atoms) relative to the z axis. If possible, can you please provide me that program or tell me how can i calculate that? Thanks in advance. Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C

[gmx-users] antechamber topologies to gromacs format

does anyone know how to conver amber topologies produced by antechamber to gromacs format? Waiting for response Anindita Gayen Senior Research Fellow University of Calcutta Bring your gang together. Do your thing. Find your favourite Yahoo! group at http://in.promos.yahoo.com/groups

[gmx-users] (no subject)

dear all, can anyone tell me how to install antechamber program on linux platform? From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/ ___ gmx-users mailing list

[gmx-users] Re: gmx-users Digest, Vol 51, Issue 77

dear sir, I am trying to do that you have said. yours sincerely, anindita ANINDITA GAYEN wrote: dear sir, I have tried to insert only one chaps in the bilayer and the problem arose after the minimisation when i started the MD. I have also tried to do a minimistaion using

[gmx-users] less number of 1-4 parameter combination

Hi all, I have built a topology file for chaps in OPLS force field with inserted hydrogen atoms along with bonds, angles, dihedrals etc parameters using the original topology from prodrg2. The problem is now, grompp results as, Generated 342378 of the 342378 non-bonded parameter combinations

[gmx-users] Meaning of CT, C_2, C_3 in ffoplsaabon.itp

--- On Mon, 23/6/08, ANINDITA GAYEN [EMAIL PROTECTED] wrote: From: ANINDITA GAYEN [EMAIL PROTECTED] Subject: To: gmx-users@gromacs.org Date: Monday, 23 June, 2008, 11:47 AM Hello Al, Can someone tell me what is the meaning of CT, CT_2, C_3, C_2 etc atomtypes defined

[gmx-users] modelling a new molecule in OPLS

I have built an all atom topology file for chaps as i have already discussed in previous mails, with charges from Gaussian DFT. The current problem is with the grompp. The error results that: processing topology... Generated 342378 of the 342378 non-bonded parameter combinations Generating 1-4

Re: [gmx-users] gromos parameterisation in OPLS

be inserting lots of hydrogens! -Justin ANINDITA GAYEN wrote: Sir, If i insert the hydrogen atoms in the first section of the itp file, where atomnames , atomtypes , nr, cgnr are displayed, wil it be wrong. Also, i was talking that, will the inclusion of ffoplsaa.itp will serve the bonded

[gmx-users] gromos parameterisation in OPLS

Hi, I came to know from the mailing list that if i only change the atomtype in the output itp file of PRODRG2 and put the charges as optimised by Gaussian; provided i include #include ffoplsaa.itp in the .top file of the new molecule and just keep the atom mumbers in [bonds], [pairs], [angles]

[gmx-users] PRODRG2 to OPLS for a new molecule

[gmx-users] Help with topology file Location: http://www.gromacs.org/pipermail/gmx-users/2003-March/004828.html [gmx-users] Help with topology file Location: http://www.gromacs.org/pipermail/gmx-users/2003-March/004846.html [gmx-users] Help with topology file Location:

[gmx-users] PRODRG2 to OPLS for a new molecule

[gmx-users] Help with topology file Location: http://www.gromacs.org/pipermail/gmx-users/2003-March/004828.html [gmx-users] Help with topology file Location: http://www.gromacs.org/pipermail/gmx-users/2003-March/004846.html [gmx-users] Help with topology file Location:

[gmx-users] PRODRG2 to OPLS for a New Molecule

[gmx-users] Help with topology file Location: http://www.gromacs.org/pipermail/gmx-users/2003-March/004828.html Score: 1000, Size: 4739 Bytes, [gmx-users] Help with topology file Location: http://www.gromacs.org/pipermail/gmx-users/2003-March/004845.html Score: 993, Size: 3578

Re: [gmx-users] gromos parameterisation in OPLS

. This is just as much work as building the topology yourself, I think. -Justin ANINDITA GAYEN wrote: Hi, I came to know from the mailing list that if i only change the atomtype in the output itp file of PRODRG2 and put the charges as optimised by Gaussian; provided i include #include

[gmx-users] RE:RE: bicelle modeling using CG MODEL

I want to simulate a peptide with nmr restraints in the bilayer containing chaps and a ganglioside, that resemble my nmr experimental results in bicelle!!!the partial charges if i want to redefine from the OPLS, i have total charge of molecule -1.577. How can i optomise the charge then?

Fw: Re: [gmx-users] bicelle gromacs MD simulation CG model?

--- On Fri, 13/6/08, ANINDITA GAYEN [EMAIL PROTECTED] wrote: From: ANINDITA GAYEN [EMAIL PROTECTED] Subject: Re: [gmx-users] bicelle gromacs MD simulation CG model? To: [EMAIL PROTECTED] Date: Friday, 13 June, 2008, 4:09 PM You can find my paper on Langmuir vol 24, Issue 10, pages 5422

Re: [gmx-users] bicelle gromacs MD simulation CG model?

: [gmx-users] bicelle gromacs MD simulation CG model? To: [EMAIL PROTECTED] Cc: Gromacs Users' List gmx-users@gromacs.org Date: Friday, 13 June, 2008, 4:50 PM ANINDITA GAYEN wrote: I have build the itp file from PRODG2 DUNDEE server. and then replaced the stom types from OPLS. Can you comment

[gmx-users] bicelle gromacs MD simulation CG model?

hi all, can someone give me information how to model a bicelle using gromacs? I have dmpc:chaps as the bicelle components, and i came to know that coarse grain model can help me. But, the picture is still not clear. Please help me to make the bicelle in gromacs. From Chandigarh to

[gmx-users] (no subject)

list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=UTF-8; format=flowed ANINDITA GAYEN wrote: hi all, can someone give me information how to model a bicelle using gromacs? I have dmpc:chaps as the bicelle components, and i came to know

RE:Re: [gmx-users] bicelle gromacs MD simulation CG model?

--- On Fri, 13/6/08, ANINDITA GAYEN [EMAIL PROTECTED] wrote: From: ANINDITA GAYEN [EMAIL PROTECTED] Subject: To: gmx-users@gromacs.org Date: Friday, 13 June, 2008, 9:56 AM Hi, I several papers of Marrink, Siewert J.; Mark, Alan E, and in a paper of Yong Jiang, bicelles are modeled

[gmx-users] genconf problem

Dear all, I have download a POPG(lip 128+Na ion 128) bilayer from http://www.softsimu.org/downloads.shtml;. I want to make a bilayer containing 128 lip/leaflate i.e, with 256 lipids having suqre surface area (X=Y). With the following commands : 1)genconf -f popg.pdb -nbox 2 2 1 -dist 0 0 0 -o

[gmx-users] bicelle modeling

hi all!!! can anyone suggest me how to model a bicelle using gromacs? From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] 1-4 Scaling Problem?

42 1 1000.0 1000.0 1000.0 43 1 1000.0 1000.0 1000.0 44 1 1000.0 1000.0 1000.0 45 1 1000.0 1000.0 1000.0 46 1 1000.0 1000.0 1000.0 #endif Is my 1-4 scaling correct? I am confused about my topologies. Please help. Ms. Anindita Gayen C/O

[gmx-users] Re: Re: water distortion above bilayer

How to be sure that the water is moving from the leaflet to the other leaflet? Can I see it from any analysis? How can i trace a water that is moving due to pbc and how to originate a pdb that will show the pdb that will be visually good for analysis (I am confused about the -pbc nojump and -pbc

[gmx-users] water distortion above bilayer

Hi all, In the TIP4P water layer above my dmpc bilayer after 100ps (OPLS-BERGER) a hole is being formed. Some water molecules are absent in the water layer, but the total no of water molecules are same. This is my semi.mdp file title = bilayer MD DMPC PURE cpp

[gmx-users] Re: gmx-users Digest, Vol 49, Issue 53 bilayer area problem

yes, the bilayer is from tielman's website. The expected area per lipid at 300K is 57nm2 to 60 nm2 where i have getting only 50 nm2. the rvdw i have used as per the rules i have read from the archive where it was said that 1.8nm to 2.0 nm should be the rvdw. Is there any problem with the

[gmx-users] bilayer DMPC

I have suffering from a problem with dmpc bilayer simulation at 300K with oplsaa-berger combination that is showing area of 50nm2 after 1.5 ns from g_energy and g_traj. I have used half-epsilon double pairlist method. the itp and mdp files are attached with. However editconf again showing the

[gmx-users] Fw: Electron Density Across the Lipid Bilayer

Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Junior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India--- On Fri, 9/5/08, ANINDITA GAYEN [EMAIL PROTECTED] wrote:From: ANINDITA GAYEN [EMAIL PROTECTED]Subject: Electron Density Across the Lipid