[gmx-users] pdb file badly broken after changing residue name a/c to amber.rtp file
Dear justin I am trying to do simulation of dna-protein complex . For this I am using amber port with gromacs-4.0.3 but for this a/c to ffamber.rtp file entry i hqve to make changes in my .pdb file residues like the DNA base name in this is only A ,C ,G,T so a/c to amber.rtp file entry I have converted it in DA,DC,DG,DT but when i have changed the name and atom name also my pdb file badly broken. Becoz after that when I have seen it in pymol viewer the structure was totally crashed . so , I want to ask you how can I get rid from this problem for doing simulation of dna-protein complexusing amber port with gromacs? so please suggest me proper methodology to make my pdb file stable even after changing residue name a/c to amber .rtp entry. Nitu harma. ___ 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
Re: [gmx-users] pdb file badly broken after changing residue name a/c to amber.rtp file
nitu sharma wrote: Dear justin I am trying to do simulation of dna-protein complex . For this I am using amber port with gromacs-4.0.3 but for this a/c to ffamber.rtp file entry i hqve to make changes in my .pdb file residues like the DNA base name in this is only A ,C ,G,T so a/c to amber.rtp file entry I have converted it in DA,DC,DG,DT but when i have changed the name and atom name also my pdb file badly broken. Becoz after that when I have seen it in pymol viewer the structure was totally crashed . so , I want to ask you how can I get rid from this problem for doing simulation of dna-protein complexusing amber port with gromacs? You probably changed the spacing when you changed the residue names. PDB files are fixed-format, according to these guidelines: http://www.wwpdb.org/docs.html -Justin so please suggest me proper methodology to make my pdb file stable even after changing residue name a/c to amber .rtp entry. Nitu harma. ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] process getting killed
Dear gromacs users, I ran a md simulation for 2ns with the mdp file as shown: er spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 5000 ; total 10 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-Protein ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp = 300.0 gen_seed = 173529 it was successful, but then while using the trajectory convert; ie, to a xtc file and also while using g_rms and g_gyrate command, it got killed. So i modified the mdp file and re-ran the md simulation for 2ns; the mdp file is: er spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 100 ; total 2 ns. nstcomm = 1 nstxout = 2500 nstvout = 2500 nstfout = 100 nstlog = 1000 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-Protein ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 igen_seed = 173529 But still it was getting killed; ie, the xtc, and xvg file conversions. Please help as to how i can overcome this problem. thank you Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/___ 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
Re: [gmx-users] process getting killed
P.R.Anand Narayanan wrote: But still it was getting killed; ie, the xtc, and xvg file conversions. Please help as to how i can overcome this problem. getting killed is a useless description for remote diagnosis. You need to read the outputs of both your MD run and your utilities and troubleshoot based on them. Mark ___ 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] 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 http://cricket.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] Doxygen
Hello, Can anybody help me to get comment from gmx source code via doxygen or there is some other way for it. Regards ___ 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
Re: [gmx-users] Doxygen
Syed Tarique Moin wrote: Hello, Can anybody help me to get comment from gmx source code via doxygen or there is some other way for it. No. You have to download the source and read it. Mark ___ 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] Atom types of OPLS-AA
Dear gmx users, I want to study polyamide using OPLS-AA force field. But for the residues, -CH2-C(=O)-NH-CH2, I can not find suitable atom types for C, H, atoms on both sides. I wonder whether OPLS-AA can model this kind of polymers. Could you give me the answer? If it is, what are they? Thank you for attention! Best regards, Chaofu Wu _ 约会说不清地方？来试试微软地图最新msn互动功能！ http://ditu.live.com/?form=TLswm=1___ 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] Arbitary small molecule for Martini force field
Dear all, I tried Martini force field and found it calculates with a good result in appearance for a *specific* calculation prepared at the Martini website. Now, I wish to use another small molecule (such as lipid) for CG simulation. Starting from the chemical structure, I draw it with MarvinSketch and save as pdb. After this I want to make a .gro file and .itp file which is compatible for Martini force field. Can u give me instruction for that? Or need (or find if possible) experimental data to tune the parameter? For my simulation the atomic simulation leads to segmentation fault (Memory: 2GB) and i feel the CG is necessary. Else if Martini is not useful for more general calculation, let me know the alternative approach for CG calculation with GROMACS. taka ___ 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
