[gmx-users] problem with angle restraints

. Please tell me where I have gone wrong. Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/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

Re: Subject: [gmx-users] error compiling mopac and gromacs

, 12 June, 2010 3:36:54 PM Subject: Re: Subject: [gmx-users] error compiling mopac and gromacs Depending on how your libmopac.a was biuld, you need the to include the f2c or g2c library as well. Gerrit Message: 5 Date: Sat, 12 Jun 2010 14:33:02 +0530 (IST) From: subarna thakur thakur.suba

[gmx-users] error in linking mopac and gromacs

According to the suggestion I have installed the f2c package in my machine.I am unable to find the g2c package. I have included the f2c library by - export LIBS=-lmopac -lf2c. But when I running  ./configure --with-qmmm-mopac --disable-float , an error is comming C compiler cannot create

[gmx-users] error compiling mopac and gromacs

/src' make: *** [all-recursive] Error 1   Please suggest where I have gone wrong.  Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un

[gmx-users] angle restraints

 restraints but I couldnot find anything about adding angle restrains. Please advice.  Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un

[gmx-users] shake and settle

Hi gmx user I want to use shake algorithm for bonds within protein and settle algorithm for the bonds of the water. How do I specify two different constraints algorithm in pr.mdp file?  Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

[gmx-users] adding constraints

Hi all, I want to add constraints for bond length of a ligand.Where do I place the constraints statement in the .rtp file or in the .top file?   Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] linc warnings

Hi My protein has a Fe4S4 cluster. I have been able to minimize the structure using Steepest descent. The log file shows following message: Steepest Descents converged to Fmax 2000 in 372 steps Potential Energy = -4.1580605e+06 Maximum force = 1.7402682e+03 on atom 820 Norm of force =

Re: [gmx-users] linc warnings

: Re: [gmx-users] linc warnings subarna thakur wrote: Hi My protein has a Fe4S4 cluster. I have been able to minimize the structure using Steepest descent. The log file shows following message: Steepest Descents converged to Fmax 2000 in 372 steps Potential Energy = -4.1580605e+06 Maximum

[gmx-users] freeze group

I running the simulation of a protein with Fe4s4 cluster. The parameters for the cluster were obtained from a previously published paper. I have been able to carry out energy minimization with the following keywords- ; cpp = /usr/bin/cpp

Re: [gmx-users] energy minimization

subarna thakur wrote: I am doing the energy minimization of a protein using the following keywords in em.mdp file- cpp                =  /usr/bin/cpp define              =  -DFLEX_SPC constraints        =  none integrator          =  steep nsteps              =  3000 ; ;    Energy

[gmx-users] energy minimization

I am doing the energy minimization of a protein using the following keywords in em.mdp file- cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 3000 ; ;Energy minimizing stuff ; emtol

[gmx-users] query regarding itp file

Hi Can any body please tell me what does c0 and c1 column represent in .itp file? And how do I obtain these parameters for a ligand. Subarna thakur The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing listgmx-users

[gmx-users] topology file in .dat format

Hello I have a gromos96 topology file for a ligand and it is in xx.dat format.How do I include this file in my gromacs version 4.0 simulation of a protein? Subarna The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing list

[gmx-users] rmsf

Hello I want to analyze the RMSF fluctuation of each residue of a protein during a simulation run. I am giving the command g_rmsf -f md.xtc -s md.tpr -b 4000 -e 6000 -o traj_rmsf.xvg -ox traj_avg.pdb. Then I am selecting the whole protein for the analysis. I am getting the RMSF per atom in the

[gmx-users] dssp programm

Hello I installed the dssp program for obtaining the secondary structure.I used the dssp programm to analyze the secondary structure of the protein after a MD simulation run. I got the out of the pogramm as m.dssp but I want to know how do I represent the output of the dssp programm graphically

[gmx-users] query regarding ffG43a1bon.itp

Hello I want to add a new bond streching parameter in the ffG43a1bon.itp file, Can anybody please tell me how the values under  Examples of usage in terms of non-bonded atom types'' determined of each bond in the file ffG43a1bon.itp   Subarna Love Cricket? Check out live scores, photos,

[gmx-users] desciption of ffG43a1bon.itp

Hello In the file ffG43a1bon.itp, the bond parameters are given like this- -- ICB(H)[N] CB[N] B0[N] ; #define gb_1 0. 1000 1.5700e+07 ; H - OA    750 ; #define gb_2 0. 1000 1.8700e+07 ; H - N (all) 895 ; #define gb_3 0.    1090  1.2300e+07 ; HC - C 

[gmx-users] parameterization of ligand

Hello I have received a parameter of a ligand of a protein from the author of an earlier published work.The parameter is in param.dat format based on ff43a1 force field.  Can anybody plz suggest how and where do I put the parameter file in the gromacs.I am using gromacs 4.0 version. Regards

[gmx-users] FeS cluster

Hello We dont have the parameters for Fe4S4 cluster in any of the the gomacs force fields but if we able to make the .itp file for the cluster manually with the help of Quantum mechanical calculations, can we place the .itp file of fe4s4 in the include section of the  protein .top file later as

[gmx-users] Fes cluster

Hello The protein I am considering is a homodimer with two chains with a Fe4S4 cluster situated at the interface of two chains with connections with both the chains by cystein residues.I have generated the .itp file of the Fe4S4 cluster and .top of the protein with pdb2gmx command.The .top

[gmx-users] problem with topolbuild execution

Hello I am trying to generate a .itp file of a Fe4S4 cluster from mol2 file with the help of topolbuild1_2_1 programm but a error is comming during execution stating Illegal characters for size information line. I dont know what is wrong with the input file. I am giving here the input mol2 file

[gmx-users] query regarding Fe4S4

Hello I have generated the individual charges of Fe4S4 cluster with Gaussian programm.I have all the interatomic distances and diherdral.I ahve also generated the .top file of the Fe4S4 cluster with the help of mktop pogramm.Can anybody please suggest how do I generated the .itp file for the

[gmx-users] query about topolgen.pl

Hi Can any body please tell me how to install and execute topolgen.pl script in linux for generationf topology file. It is not given in the Readme file. Subarna Love Cricket? Check out live scores, photos, video highlights and more. Click here

[gmx-users] query regarding .top file

Hello I have generated .top file for an ligand with the mktop programm for OPLSAA force field , how do I include this .top file for the ligand along with that my protein in the gromacs run? Subarna Looking for local information? Find it on Yahoo! Local

[gmx-users] problem with installation of topolbuild1.2.1

Hi Can anybody please tell me how to install topolbuild 1.2.1 programm in  32 bit machine with Fedora linux operating system. I cannot understand the instruction given in the READ ME file Subarna  See the Web#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz.

[gmx-users] choosing force filed

Hello Can any body please suggest which force field would be appropiate for simulation of protein with Fe-S cluster? Can I use the  opls-aa force field for such simulations? Subarna Love Cricket? Check out live scores, photos, video highlights and more. Click here

[gmx-users] parameters of Fe-S cluster

Hello Does anyone have the topology parameters for Fe-S cluster ? Subarna ICC World Twenty20 England #39;09 exclusively on YAHOO! CRICKET http://cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] problem of getting with Dssp

Hi I want to install dssp programm in my linux machine but I am not getting it from the website http://swift.cmbi.ru.nl/gv/dssp/. The linux executable given in the website does not seems to work.Can any one suggest any alternative site for downloading the current version of dssp. Subarna

[gmx-users] Problem wih Fe-S cluster

Hi everyone I am facing a problem with derivation of parameters of Fe-S cluster in a protein.Can anybody please tell me for deriving a parameters do I have to consider the co-ordinates of a typical fe-s cluster as there in Protein Data Base (PDB) or the co-ordinates of the Fe-S cluster present 

[gmx-users] gromos type in .rtp file

hello everyone Can any body please explain to me, what does the trm gb_38 or gb_39 stand for under the bond coulmn of the .rtp file ? what is gromos type under angles and impropers? Subarna Explore and discover exciting holidays and getaways with Yahoo! India Travel

[gmx-users] problem with FeS cluster

Hello user Can anybody please tell me how to prepare a topology file for the FES4 cluster incorporated in a protein Subarna Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com___ gmx-users mailing list

Re: [gmx-users] problem with FeS cluster

To: Discussion list for GROMACS users gmx-us...@gromacs..org Sent: Wednesday, 3 June, 2009 4:46:37 PM Subject: Re: [gmx-users] problem with FeS cluster subarna thakur wrote: Hello user Can anybody please tell me how to prepare a topology file for the FES4 cluster incorporated in a protein   I

[gmx-users] problem with generation of .gro file

the error? How to modify the rtp file to consider the ligand?  Subarna thakur University of north bengal Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo..com___ gmx-users mailing listgmx-users