[gmx-users] protein domain separate
Hi As I told in my perevious mail, My system consist of a 2-domain protein (Domain A and B), even when I did EM minimization this 2 damain separated. my em.mpf is: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 4 constraint_algorithm = shake shake_tol = 0.0001 nstenergy = 10 nstxtcout = 10 nstlist = 5 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb= 1.2 rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Energy minimizing stuff ; emtol = 10.0 emstep = 0.01 Also it is not because of pbc, What do you suggest for solving this, thank you very much for replying. -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ 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] protein domain separate
hazizian wrote: Hi As I told in my perevious mail, My system consist of a 2-domain protein (Domain A and B), even when I did EM minimization this 2 damain separated. No they didn't. Check the website. my em.mpf is: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 4 constraint_algorithm = shake shake_tol = 0.0001 nstenergy = 10 nstxtcout = 10 nstlist = 5 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb= 1.2 rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Energy minimizing stuff ; emtol = 10.0 emstep = 0.01 Also it is not because of pbc, What do you suggest for solving this, thank you very much for replying. -- Tehran University of Medical Sciences www.tums.ac.ir -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ 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] number of opposition ions
For neutralization of system (pr + dna), what number of ions with opposition on must be used? How do I understand this number? ___ 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] reduced units
On Sat, Oct 17, 2009 at 06:10, lammps lammps lammp2fo...@gmail.com wrote: Dear, I want to do stochastic simulations in the framework of Langevin dynamics using Gromacs with the reduced units. The questions are: 1. How to turn on the reduced units? Is there any parameters for setting? I am not sure I understand. For Langevin dynamcis/thermostat use: integrator = SD bd-fric=0; Read the manual about the relations between dt tau-t, I use 5e-4 2, respectively. Hope I helped. Omer. ___ 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] number of opposition ions
leila karami wrote: For neutralization of system (pr + dna), what number of ions with opposition on must be used? How do I understand this number? pdb2gmx or grompp will probably report net charges if non-zero. 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] Is the time scale of the protein domain motion within nano-second?
Hi Is the time scale of the protein domain motion within nano-second? Thank you Lin ___ 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] Is the time scale of the protein domain motion within nano-second?
Chih-Ying Lin wrote: Hi Is the time scale of the protein domain motion within nano-second? Not typically, these motions usually occur more on the time scale of a microsecond (or more). It will depend on how large the protein is, and what amplitude the motion is, though, so I suppose anything is possible. Domain motions are more often analyzed by normal mode analysis or elastic network models, because typical solution MD doesn't achieve the appropriate time scale. -Justin Thank you Lin ___ 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
Re: [gmx-users] Example file for DNA
Hi,
I stripped the following from a script of mine. The original script
did some additional things before, involving first a conversion from
PDB to CNS format and later to GMX format. I rearranged it without
testing. You can try it and if you find that it doesn't do a proper
job, you can send me the before and after file.
Hope it helps (hope it works ;))
Tsjerk
###
#!/bin/bash
# RENAME RESIDUES
DNA_PDB2GMX='s/\(^.\{17\}\)DG /\1DGUA/; s/\(^.\{17\}\)DA /\1DADE/;
s/\(^.\{17\}\)DC /\1DCYT/; s/\(^.\{17\}\)DT /\1DTHY/'
RNA_PDB2GMX='s/\(^.\{17\}\) G /\1 GUA/; s/\(^.\{17\}\) A /\1 ADE/;
s/\(^.\{17\}\) C /\1 CYT/; s/\(^.\{17\}\) U /\1 URA/'
# RENAME ATOMS AND DELETHE HYDROGENS
NUCL_DELHYD=/^.\{13\}H.'/d; /^.\{13\}H7..THY/d; /^.\{12\}H5''/d
THY_C72C5M='s/\(^.\{13\}C\)7 .THY/\15M.THY/'
NUCL_PDBS2GMX=$NUCL_DELHYD; $THY_C72C5M; s/\(^.\{12\}...\)'/\1\*/
sed -e { $NUCL_PDB2GMX; $DNA_PDB2GMX; $RNA_PDB2GMX } $1
On Sat, Oct 17, 2009 at 3:08 AM, Justin A. Lemkul jalem...@vt.edu wrote:
David Crosby wrote:
Hello fellow GROMACS users!
I've been having a heck of a time with the reformatting of a DNA molecule
into a GROMACS-compatible format. I know that residues (bases) must be
renamed to DTHR, etc., though it would be endlessly helpful if someone
could
please send me an example pdb or gmx file I can use as reference. Better
yet, if anyone has a nifty program that will reformat a nucleic acid model
into the GROMACS format, that would answer my prayers! The duplex I'm
working with is only 21nt, so it's not insane to have to modify the file
by
hand...
A simple Perl script can make substitutions, or you can use a text editor
like vi or a command like sed. In about 4 commands, the whole file can be
re-named. In vi, for example:
:1,$s/DT /DTHY/g
...and all of your thymines are re-named (note the spacing is important).
-Justin
Thanks in advance!
Dave Crosby
University of California, Irvine
Dept of Pathology and Laboratory Medicine
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--
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
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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