[gmx-users] .rtp file

Hello, I ve a query.I ve not created .rtp file,.atp file.I ve only .pdb file and i used pdb2gmx command and successfully got .top,.itp and .gro file. Do my files contains error without making use of .rtp and .atp files.Its just a curiosity to know.And how to make .rtp and .atp files. thanx. --

[gmx-users] difference in forcefields.

Hello Users, I am facing a problem in obtaining topologies for my ligand.I tried working on acpype,bt it seems very complex to me.PRODRG is easy but it uses gromos87 force field.PRODRG 2.5 is still not available for download. can anyone suggest me how to obtain topologies for my protein and ligan

[gmx-users] Estimation of free energy using Linear Response method

Dear Gromacs Users, I would like to ask how the Linear Response method can be applied for the calculation of free energy using the Gromacs package? More specifically, I am interested in the set-up of the MD protocol and the parameters of the input files. Thanks in advance for your help-- gmx-

[gmx-users] The time correlation functions for the orientation of the C-H

Hi GMX users, I am interesting to compute the tcf of C-H bonds for several surfactants in micelles. Is there a tool in GROMACS to do that ? Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http:

Re: [gmx-users] PRODRG2.5 server not found.

swati patel wrote: Helo Justin, The link for prodrg 2.5 server is i.e. http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta is 404 not found.How should I proceed further? http://davapc1.bioch.dundee.ac.uk/prodrg/ -Justin -- Justin A. Lemkul Ph

Re: [gmx-users] .rtp file

ibi2010...@iiita.ac.in wrote: Hello, I ve a query.I ve not created .rtp file,.atp file.I ve only .pdb file and i used pdb2gmx command and successfully got .top,.itp and .gro file. Do my files contains error without making use of .rtp and .atp files.Its just a curiosity to know.And how to make

[gmx-users] PRODRG server

Hello Justin, Sorry for again and again bothering you.But in prodrg2.5 server,there is no option to choose force fields.It automatically generates topology in gromos 87 force fields. I am using 4.5 version of gromacs in which gromos force fields are gromos 96.How to match my protein and ligand to

Re: [gmx-users] PRODRG server

swati patel wrote: Hello Justin, Sorry for again and again bothering you.But in prodrg2.5 server,there is no option to choose force fields.It automatically generates topology in gromos 87 force fields. The default force field used by the latest PRODRG is Gromos96 43a1, not Gromos87. -J

[gmx-users] (no subject)

Hello, I got all confused.So i started with the beginnning.i generated topology for my protein Streptavidin and generated topology for my ligand using prodrg2.5 server. I am getting error at step editconf i.e.Fatal error:Something is wrong in the coordinate formatting of file conf.gro. Any sugge

Re: [gmx-users] Gromacs 3D maps

On 18/11/2011 12:24 AM, Alex wrote: Dear all, I'd like to transform an md gromacs trajectory in a 3d maps set. I mean that every 100ps, I need to export frame coordinates to a 3d map. Than I need to compare a map with the following. Could give me any advice about tools/software to use? I don't

Re: [gmx-users] (no subject)

ibi2010...@iiita.ac.in wrote: Hello, I got all confused.So i started with the beginnning.i generated topology for my protein Streptavidin and generated topology for my ligand using prodrg2.5 server. I am getting error at step editconf i.e.Fatal error:Something is wrong in the coordinate forma

Re: [gmx-users] problem obtaining similar force fields for protein and ligand

On 18/11/2011 6:54 PM, swati patel wrote: Hello Users, I am facing a problem in obtaining topologies for my ligand.I tried working on acpype,bt it seems very complex to me.PRODRG is easy but it uses gromos87 force field.PRODRG 2.5 is still not available for download. can anyone suggest me ho

Re: [gmx-users] analysing helix dynamics

On 18/11/2011 1:54 PM, jayant james wrote: Hi all, During MD simulations of a protein,I find that there are two helices switch periodically from being parallel and perpendicular to each other. I'd like to plot out the orientation of these two helices with respect to each other, is there a comman

Re: [gmx-users] non-specific protein-protein interactions

On 18/11/2011 8:10 AM, Ben Reynwar wrote: Dear gromacs list, Does anyone know how well current force fields capture the energetics of non-specific protein-protein interactions? I'm simulating a protein with an arm that alternates between (apparently) non-specific adsorption to the main-body of

Re: [gmx-users] query for energy minimization in solvent

On 18/11/2011 7:40 AM, Anushree Tripathi wrote: Yes I m using 4.0.7 version.so for that how could I change the name accordingly. You used it in your [molecules] section. Change it to what it should be, per ions.itp. Mark On Sat, Nov 5, 2011 at 1:37 AM, Justin A. Lemkul

Re: [gmx-users] what's the math algorithm?

On 18/11/2011 7:29 AM, Liu, Liang wrote: Dear all, Assuming I have a some tabulated potentials, table.xvg, tablep.xvg, table_P_P.xvg, table_P_C.xvg and so on. Also there are non-zero values in the first column of both table.xvg and tablep.xvg; while the first column (x), the six column (h(x))

[gmx-users] fatal error occuring.

Hello Justin, After setting up grompp command,i am getting an error "Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = 1, while at->nr = 1179)".I am heading up step by step taking your aid. What should i do?How to correct it?? Thanx. ---

Re: [gmx-users] Hydrogen database

On 18/11/2011 3:11 AM, Ehud Schreiber wrote: Hi, I have recently studied the hydrogen database format of .hdb files (page 118, section 5.6.4 in the manual version 4.5.4). I would like to make a few remarks that, if correct, may need addressing. 1)Method 3 of adding the hydrogens, that of tw

[gmx-users] Issue in membrane simulation How To

Hi all, I was checking the how to on membrane proteins, and i think there is a little error in the section "Increasing the size of the water segment in the z-direction" The line # |cat not_last_line.gro new_waters.gro last_line.gro > new_system.gro| following the notation of the tutorial, recre

Re: [gmx-users] fatal error occuring.

ibi2010...@iiita.ac.in wrote: Hello Justin, After setting up grompp command,i am getting an error "Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = 1, while at->nr = 1179)".I am heading up step by step taking your aid. What should i do?How to correct it?? Without s

[gmx-users] fatal error occuring.

Hello Justin, Somehow I obtained ligand and protein topology in charmm force fields. After command grompp,I am getting an error "No such moleculetype LIG" where lig is my ligand abbreviation. Any suggestions for my error?? Thanx. -- gmx-users mailing listgmx-users@gromacs.org http://lists.

Re: [gmx-users] fatal error occuring.

swati patel wrote: Hello Justin, Somehow I obtained ligand and protein topology in charmm force fields. After command grompp,I am getting an error "No such moleculetype LIG" where lig is my ligand abbreviation. Any suggestions for my error?? Have you done the proper tutorial material? T

[gmx-users] Extract van der waals surface atoms coordinates

Dear All   How can I extract van der waals surface atoms coordinates from MD Trajectory and write them to a file? Is it possible with gromacs? And with other tools? Any suggestion?   Thanks in advance-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

Re: [gmx-users] Extract van der waals surface atoms coordinates

Alex Jemulin wrote: Dear All How can I extract van der waals surface atoms coordinates from MD Trajectory and write them to a file? Is it possible with gromacs? And with other tools? g_sas -i produces a topology of surface atoms, from which you can get atom numbers, create an index file,

Re: [gmx-users] Poor exchange probability for REMD

On 18/11/2011 12:43 PM, ÏéÇ« ¿× wrote: Dear GMX users， Recently i am performing the REMD simulation with Gromacs program and the temperature distribution for each replica was predicted with the server "http://folding.bmc.uu.se/remd/";. However, after a 2-ns short test simulation with 64 re

[gmx-users] g_lie question

I am trying to figure out how to use the g_lie tool in gromacs. I have the dGbind value for the ligand-solvent interactions and for the protein-ligand complex. However, I cannot find in the manual what units these values are. I get the following: DGbind = 1953867.080 (0.664) and DGbind = 185147

Re: [gmx-users] GROMACS/ORCA QMMM

Hi Justin, I tried using a larger step size but my system blew up... My guess is that I have a bad starting structure, I'll work on the initial structure for the QM region (energy minimize). When I'm running ORCA I want to have a LJ file to correct for the interaction of my QM system with the pr

[gmx-users] Re: g_lie question

I see from the file that the units are in KJ/mol, which means my calculations are really off. But regardless, I still don't understand what the value in parentheses means, like (nan). If anyone can decipher, please respond. Thank you for your time. 2egy On Nov 18, 2011, at 11:43 AM, EGY wrote:

[gmx-users] How DispCorr influsnces pressure

Dear all: Could anybody comment about why "DispCorr=EnerPres" influences pressure so drastically? For certain system of liquid/vapor interface, we get P_zz (perpendicular to the interface) = -7 (with correction) and +4 without correction. The statistics is a few nanoseconds, so this cannot be just

Re: [gmx-users] How DispCorr influsnces pressure

On 2011-11-18 19:52, Dr. Vitaly V. Chaban wrote: Dear all: Could anybody comment about why "DispCorr=EnerPres" influences pressure so drastically? For certain system of liquid/vapor interface, we get P_zz (perpendicular to the interface) = -7 (with correction) and +4 without correction. The stat

[gmx-users] .ppa file

Hello Justin, I am doing project on afm simulation of protein complex.I have used em.mdp file for minimization. Now i am wondering where to use .ppa file for afm parameters. Can you guide me with files related to afm simulation. - This email has been sen

Re: [gmx-users] How DispCorr influsnces pressure

> Dispcorr is only for homogeneous liquids. It should not be used for > membranes. More precisely -- the dispersion correction is an analytical correction to both the pressure and energy that is rigorously correct in the limit of the radial distribution function g(r)=1 outside the van der Waals cu

Re: [gmx-users] Re: g_lie question

EGY wrote: I see from the file that the units are in KJ/mol, which means my calculations are really off. But regardless, I still don't understand what the value in parentheses means, like (nan). If anyone can decipher, please respond. Thank you for your time. "nan" mean "not a number," indi

Re: [gmx-users] .ppa file

ibi2010...@iiita.ac.in wrote: Hello Justin, I am doing project on afm simulation of protein complex.I have used em.mdp file for minimization. Now i am wondering where to use .ppa file for afm parameters. Can you guide me with files related to afm simulation. The .ppa format has not been

Re: [gmx-users] non-specific protein-protein interactions

On Fri, Nov 18, 2011 at 7:23 AM, Mark Abraham wrote: > On 18/11/2011 8:10 AM, Ben Reynwar wrote: >> >> Dear gromacs list, >> >> Does anyone know how well current force fields capture the energetics >> of non-specific protein-protein interactions?  I'm simulating a >> protein with an arm that alter

[gmx-users] afm simulation

Hello, I went through the tutorial umbrella sampling and i found that it is similar to afm simulation only using harmonic potential. May be i am wrong.Can you just satisfy my curiosity? Thanx. - This email has been sent using ArithMail at "Indian Instit

Re: [gmx-users] afm simulation

ibi2010...@iiita.ac.in wrote: Hello, I went through the tutorial umbrella sampling and i found that it is similar to afm simulation only using harmonic potential. May be i am wrong.Can you just satisfy my curiosity? They are functional equivalents. -Justin --

[gmx-users] Hbond occupancy

Greeting Is there a value from it we can be sure about hbond existence in reality. For example for a hbond occupancy rate of 10% we can say that this hbond has a good chance to exist in reality an effectively participate in the protein phenomena (movement,structure...) and for another hbond occ

[gmx-users] REMD: when it exchange the replica, it will be bombed!!

dear teachear, i do remd in NPT, when it exchange the replica, it will be bombed!! step 400, will finish Wed Nov 23 23:21:34 2011 Warning: 1-4 interaction between 1384 and 1396 at distance 140.157 which is larger than the 1-4 table size 20.895 nm These are ignored for the rest of the simulatio

Re: [gmx-users] REMD: when it exchange the replica, it will be bombed!!

On 19/11/2011 1:49 PM, 杜波 wrote: dear teachear, i do remd in NPT, when it exchange the replica, it will be bombed!! step 400, will finish Wed Nov 23 23:21:34 2011 Warning: 1-4 interaction between 1384 and 1396 at distance 140.157 which is larger than the 1-4 table size 20.895 nm These are

Re: [gmx-users] non-specific protein-protein interactions

On 19/11/2011 6:42 AM, Ben Reynwar wrote: On Fri, Nov 18, 2011 at 7:23 AM, Mark Abraham wrote: On 18/11/2011 8:10 AM, Ben Reynwar wrote: Dear gromacs list, Does anyone know how well current force fields capture the energetics of non-specific protein-protein interactions? I'm simulating a pro

[gmx-users] simulation of a simple, solvated DPPC membrane

Hello there! I am an undergraduate working on my thesis, which involves the simulation of a DPPC membrane. My college is small and the department does not have experience with MD simulations, so I am 100% on my own. I have successfully modeled simple proteins in water- but I want to move onto bila

Re: [gmx-users] simulation of a simple, solvated DPPC membrane

undergrad j wrote: Hello there! I am an undergraduate working on my thesis, which involves the simulation of a DPPC membrane. My college is small and the department does not have experience with MD simulations, so I am 100% on my own. I have successfully modeled simple proteins in water- bu

Re: [gmx-users] non-specific protein-protein interactions

On Fri, Nov 18, 2011 at 8:07 PM, Mark Abraham wrote: > On 19/11/2011 6:42 AM, Ben Reynwar wrote: >> >> On Fri, Nov 18, 2011 at 7:23 AM, Mark Abraham >>  wrote: >>> >>> On 18/11/2011 8:10 AM, Ben Reynwar wrote: Dear gromacs list, Does anyone know how well current force fields ca