[gmx-users] how to include Fe-S topology in .rtp file
hi all... I am simulating a protein with Fe-S cluster. What is the protocol for generating a .rtp file with Fe-S topology...As i am using ffG43a1 forcefield.. i searched FFG43a1bon.itp file for Fe-S bond, angle and dihedral type... but it is not there..what i should do?.. If anyone have the idea of the procedure..please outline me the procedure.. Thanks.. Amrita Ph.D scholar, Burdwan University. Own a website.Get an unlimited package.Pay next to nothing.*Go to http://in.business.yahoo.com/___ 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 interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to include ionic strength
Dear gromacs users, I am simulating a protein which works in salt solution within cell. I have to include 4M salt (say, NaCl) to the simulation box. How can i include such ionic strength? Please outline me the procedure. Thanks in advance. Amrita Paul Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to do MD simulation of protein with Fe-S cluster
Dear Gromacs users, I am currently working on Dynamic simulation studies using GROMACS software. In my current work I want to do simulation of a protein containing Fe-S cluster. If i directly do through pdb2gmx then it is giving a error massage like "FES in not included in .rtp file". Regarding this I went through the Article "Gromacs Tutorial for Drug-Enzyme Complex" which has shown clearly step-by-step how to include new topologies for drug/ligand molecules. But I was not successful in running the dynamics. The "Drug-Enzyme complex" tutorial was specific for ligands/Drugs that do not form part of the protein chain. But if I want to include topology for Fe-S cluster which occur within the protein chain, how to do it? I tried according to the tutorial but was unsuccessful all the time. I'll be very grateful if you can outline me the procedure to be followed in such cases. Thank you, Amrita Paul Bollywood news, movie reviews, film trailers and more! Go to http://in.movies.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] about md simulation
Dear colleagues, I am simulating a phosphorylated protein embedded in waterbox. When I try running mdrun, I get a LINCS warning. Does this mean that I have go back to the CG-EM step and use the double precision libs? The md.log file reads: Initializing LINear Constraint Solver number of constraints is 2365 average number of constraints coupled to one constraint is 2.5 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.336565 691 696 0.033770 After LINCS 0.342830698700 0.028042 Step -1, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.858278 (between atoms 3397 and 3398) rms 0.016634 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3395 3398 76.20.1341 0.0446 0.1470 3398 3399 78.80.1341 0.0492 0.1470 Constraint error in algorithm Lincs at step -1 Grid: 10 x 10 x 10 cells Configuring nonbonded kernels Testing x86_64 SSE supports...presents Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 70.089874 1537 1456 0.559021 After LINCS 29.983810 3223 32240.787549 Like this, errors showed "Constraint error in algorithm Lincs at step 0, step1" and the simulation stops at step 1. Do I have to modify my md.mdp to remedy this? Your advice is appreciated. Best regards, Amrita Ghosh National Institute of Mental Health and Neurosciences, Bangalore-29. India. 5, 50, 500, 5000 - Store N number of mails in your inbox. Go to http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] about md simulation
Dear colleagues, I am simulating a phosphorylated protein embedded in waterbox. When I try running mdrun, I get a LINCS warning. Does this mean that I have go back to the CG-EM step and use the double precision libs? The md.log file reads: ... Initializing LINear Constraint Solver number of constraints is 2365 average number of constraints coupled to one constraint is 2.5 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.336565 691 696 0.033770 After LINCS 0.342830698700 0.028042 Step -2, time -0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.342830 (between atoms 698 and 700) rms 0.028042 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 687 689 34.60.17760.1937 0.1330 689 690 34.70.1079 0.0919 0.1000 -- Constraining the coordinates at t0-dt (step -1) Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.095785 3223 3224 0.006243 After LINCS 0.858278 3397 3398 0.016634 Step -1, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.858278 (between atoms 3397 and 3398) rms 0.016634 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3395 3398 76.20.1341 0.0446 0.1470 3398 3399 78.80.1341 0.0492 0.1470 Constraint error in algorithm Lincs at step -1 Started mdrun on node 0 Tue Sep 11 07:03:49 2007 Initial temperature: 420.799 K Step Time Lambda 00.00.0 Grid: 10 x 10 x 10 cells Configuring nonbonded kernels Testing x86_64 SSE supports...presents Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 70.089874 1537 1456 0.559021 After LINCS 29.983810 3223 32240.787549 Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 227.983810 (between atoms 3223 and 3224) rms 4.787549 atom 1 atom 2 angle previous, current, constraint length 3395 3398 76.20.1341 0.0446 0.1470 3398 3399 78.80.1341 0.0492 0.1470 Constraint error in algorithm Lincs at step 0 Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 227.983810 (between atoms 3223 and 3224) rms 4.787549 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3395 3398 76.20.1341 0.0446 0.1470 3398 3399 78.80.1341 0.0492 0.1470 Constraint error in algorithm Lincs at step 1 and the simulation stops at step 1. Do I have to modify my md.mdp to remedy this? Your advice is appreciated. Best regards, Amrita Ghosh National Institute of Mental Health and Neurosciences, Bangalore-29. India. -- title = Full mdp run sample cpp = /lib/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! steps = 20 ; total 100 ns ;nstcomm = 1 nstxout = 500 nstvout = 1000 nstfout = 0 nstlog = 500 nstenergy = 500 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.4 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps = protein sol NA+ ref_t = 300 300 300 ; Energy monitoring energygrps = protein sol NA+ ; Pressure coupling is on Pcoupl = berendsen pcoupltype = anisotropic tau_p =0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 Get the freedom to save as many mails as you wish. To know how, go to http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html___ gmx-users mailing listgmx-users@gromacs.org http://www.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 interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
