[gmx-users] query for g_sas
Hello gmx users, I suppose this is one of the more common subject post going around in the mailing list. I have gone through the list and have gathered some information on the subject. But I have some queries and if someone can shed light on it, it will be of great help to me. I am presently trying to calculate the sasa for specific residues as a function of time from my simulation trajectory.I am using g_sas tool from gromacs ver3.3 for the purpose.I wanted to check the values it generated. So I created a gly-X-gly tripeptide in an extended conformation and calculated the sasa for the twenty amino acids.I also calculated the same using the tool naccess.I then compared the two values with the value reported earlier for the various amino acids (J. Mol. Biol.196:641-656(1987)) Values for some of the amino acids are as: jmb Gromacs3.3 Naccess Ala 113 100 115 Arg 241 211 246 Asn 158 133 155 Asp 151 132 151 Cys 140 121 140 It seems the values from naccess and jmb(reported in J. Mol. Biol) are similar.I suppose one of the factor for the difference in values between naccess and gromacs3.3 could be because of the different VDW radii used for the atoms. Naccess uses Chothia's VDW radii whereas Gromacs3.3 uses the VDW radii as reported in gmx_sas.c. Is it the case? Can I go ahead and perform the calculation using this tool? I have come accross papers which have used g_sas tool for performing the sasa calculation for the entire protein or peptide. Can anyone refer to me some papers where sasa calculation has been done for specific residues using g_sas. I have also read in the mailing list that differnet versions of Gromacs give different sasa values.people seem to report that values from Ver3.3, ver3.3.1 and ver3.3.2 are different. I haven't used 3.3.1 or 3.3.2. So what is the update in this front.Previous people who have gone through this, please help me out. Finally I also read in the list about the flexibility of chossing the VDW radii options. Has anything been done yet? Thank you. -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular Simualtion lab, Dept. of BSBE;IITK-kanpur, Uttar pradesh,India-208016. email:[EMAIL PROTECTED],[EMAIL PROTECTED] mob:09415473973 ___ 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] TFE query
Hello gmx users, I have a query and would be greatfull if I could get some suggestions on the subject. I constructed a tfe.itp file with the parameters mentioned by Fioroni et. al., J. Phys. Chem. B 2000, 104, 12347-12354. I then generated a tfe.gro file using InisghtII molecular modeling package followed by genconf. I ran a energy minimization fand then a 2ns NPT ensemble Molecular Dynamics simulation on the system. My Parameter file is as follows: title = equilibration cpp = /lib/cpp integrator = md dt = 0.002; ps ! nsteps = 100 ; total 2ns nstcomm = 1 nstxout = 500 nstvout = 5 nstfout = 0 nstxtcout = 500 xtc_precision = 1000 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid pbc = xyz rlist = 0.8 rcoulomb= 1.4 rvdw= 1.4 ; Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 0.1 tc-grps = TFE ref_t = 300 energygrps = TFE ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 4.0 compressibility = 1.22e-4 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 I did not specify Lincs algorithm in the parameter file to constrian the bonds, rather I used [constraints] for bond distance in the tfe.itp file itself. I tried using tau_p as 1ps to 3 ps, but in doing so, my simulation crashed after a certain period with the error message as high pressure scaling, and the failure of the constraint algorithm (either lincs or shake). So I used tau_p as 4 ps which is the value used for simulation in the paper mentioned above. The isothermal compressibility for liquid TFE at 298K is 1.22e-4 The density of TFE at 298K is 1383 Kg/m3. These values are mentioned in the paper. I then calculated the Properties Temperature, pressure and density for the simulation using g_energy.The average vaules for the properties are as: Temperature: 300.67 Density: 1402.95 Pressure: -2.59 Is the density value reasonable??? Why is the pressure value so different? I would be very greatfull If I could get some suggestions on the parameters and on the values of the properties mentioned. Thank you. -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular Simualtion lab, Dept. of BSBE;IITK-kanpur, Uttar pradesh,India-208016. email:[EMAIL PROTECTED],[EMAIL PROTECTED] mob:09415473973 ___ 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] Generating a solvent box
Hello gmx users, I have a query to ask.It would be nice if someone could suggest me on this.I have a tfe molecule generated using InsightII program package.Now I would like to create a box containing a fixed number of tfe molecules based on its density.I tried using genbox and genconf for the purpose but am not able to achieve my aim.If someone has tried to do this before and have some idea, I would be thankfull if you could shed some light on the subject. Thanking you. -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular Simualtion lab, Dept. of BSBE;IITK-kanpur, Uttar pradesh,India-208016. email:[EMAIL PROTECTED],[EMAIL PROTECTED] mob:09415473973 ___ 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
Re: [gmx-users] Generating a solvent box
Hello justin, Here is what I did.I initially defined a cubic box into which I placed the TFE molecule.This I did using editconf.Then I used genconf with the follwing command. genconf_mpi -f tfe-box-four.gro -o out-four.pdb -nbox 5 5 5 Yes I am able to generate a regular arrangment of the TFE molecules. But what I want to do now is to have a predfined cubic box dimension which I want to solvate with a fixed number of TFE molecules corresponding to a given density. Thanks for your response. Quoting Dilraj Lama [EMAIL PROTECTED]: Hello gmx users, I have a query to ask.It would be nice if someone could suggest me on this.I have a tfe molecule generated using InsightII program package.Now I would like to create a box containing a fixed number of tfe molecules based on its density.I tried using genbox and genconf for the purpose but am not able to achieve my aim.If someone has What did you try (i.e., what commands did you issue)? You should be able to generate at least a regular arrangement of TFE molecules with genconf. tried to do this before and have some idea, I would be thankfull if you could shed some light on the subject. Thanking you. -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular Simualtion lab, Dept. of BSBE;IITK-kanpur, Uttar pradesh,India-208016. email:[EMAIL PROTECTED],[EMAIL PROTECTED] mob:09415473973 ___ 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 -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://bevanlab.biochem.vt.edu/Pages/Personal/justin/ =___ 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 -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular Simualtion lab, Dept. of BSBE;IITK-kanpur, Uttar pradesh,India-208016. email:[EMAIL PROTECTED],[EMAIL PROTECTED] mob:09415473973 ___ 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] query regarding methanol density
Hello gmx users, I want to perform a simulation study of a peptide solvated in methanol using Gromacs 3.2.1 package with gromos96 43a1 forcefiled.For the purpose I choose the methanol.itp for the parameters of methanol.I am using the methanol216.gro contributed by Bert de Groot. I have set up system with the peptide solvated in a cubic methanol box.The density of the sysytem is now reported to be about 764.677 g/l.My query is, is it ok for me to perform the simulation with the mentioned density?? Thank you all. -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular Simualtion lab, Dept. of BSBE;IITK-kanpur, Uttar pradesh,India-208016. email:[EMAIL PROTECTED],[EMAIL PROTECTED] mob:09415473973 ___ 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
Re: [gmx-users] Restart
I know this will get an rtfm response, however, I am writing this after looking at the online help pages and perusing the email archive. Simply put, I have a 750 ps simulation that I want to run for another 750 ps. Is there a clear explanation somewhere for how one should do this? use tpbconv with -extend option Specifically, if I shut off the gen_vel option in my mdp file and use the the -t option to specify my first trajectory file are these the only changes necessary? If I keep all other options identical will I get the 750 ps continuation I desire? There is no need to change the mdp file.Have a look at the tpbconv options. Thanks for the help. Mark ___ 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 -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular Simualtion lab, Dept. of BSBE;IITK-kanpur, Uttar pradesh,India-208016. email:[EMAIL PROTECTED],[EMAIL PROTECTED] mob:09415473973 ___ 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] Generalized order parameter S2
Hello gmx-users, I have a query regarding the generalized order paprameter S2.I have performed a 50ns simulation of a protein in solution.I now want to calculate the order parameter S2 of the protein from the trajectory.I looked through the mailing list to get an idea on how to go about calculating the property. I collected information that the tools g_chi and g_rotacf can help me perform the task. g_chi uses Phi, Psi and Omega angles to calculate it. g_rotacf can calculate it with respect to N-H bond angle. Which of the two approach would be more appropriate? Also using g_rotacf I am still not very clear on how to go about using the tool. Can anyone who has previuosly performed this calculation help me out. I look forward to your responses. Thank you. -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular Simualtion lab, Dept. of BSBE;IITK-kanpur, Uttar pradesh,India-208016. email:[EMAIL PROTECTED],[EMAIL PROTECTED] mob:09415473973 ___ 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] References for globular protein simulation using PME
Dear all gmx-users, I have been trying to dig out some well cited paper on simulation of globular protein using PME .Can anyone please suggest to me some references I can look out for. Thanks to all. -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular Simualtion lab, Dept. of BSBE;IITK-kanpur, Uttar pradesh,India-208016. email:[EMAIL PROTECTED],[EMAIL PROTECTED] mob:09415473973 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] defining 2 posres at a time in mdp
define them in the same line. define = -DPOSRES_WATER -DPOSRES hi all, I want to define position restraints for a part of protein and water molecules also. I need to deinfe -DPOSRES and -DPOSRES_WATER at the same time. When I do it on separate lines in the mdp file, only first line is being read and accepted. Is there any way to include both of them in the same mdp file simultaneously. regards anwar - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular Simualtion lab, Dept. of BSBE;IITK-kanpur, Uttar pradesh,India-208016. email:[EMAIL PROTECTED],[EMAIL PROTECTED] mob:09415473973 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
