Re: [gmx-users] cross correlations
Thanks a lot Sir for your help. On Fri, Jun 24, 2011 at 22:54, Tsjerk Wassenaar wrote: > Hi Bipin, > > Read them in as a vector of numbers and divide them into sqrt(len(vector)) > rows to get yourself a nice square correlation matrix. > > Cheers, > > Tsjerk > > On Jun 24, 2011 3:28 PM, "bipin singh" wrote: > > Hello, > I have some doubts regarding the output file correl.dat as it contains 3 > columns, but I am not able to get what are > these column contains,I mean how to change it to the format in which I can > directly plot the data to get DCCM map... > For e.g in this form > Res1 Res2 Correlation coefficient > x yz > > On Sun, Jun 19, 2011 at 16:16, Tsjerk Wassenaar wrote: > > > Of course you did.. > --- > *Regards,* > Bipin Singh > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] cross correlations
Hello, I have calculated the covariance matrix for C-alpha atoms(179 aa) only,but after plotting the correlation, I have observed that it is of 537X537,instead of179X179.Please suggest me how to get correlation between the C-alpha atoms only. On Fri, Jun 24, 2011 at 22:54, Tsjerk Wassenaar wrote: > Hi Bipin, > > Read them in as a vector of numbers and divide them into sqrt(len(vector)) > rows to get yourself a nice square correlation matrix. > > Cheers, > > Tsjerk > > On Jun 24, 2011 3:28 PM, "bipin singh" wrote: > > Hello, > I have some doubts regarding the output file correl.dat as it contains 3 > columns, but I am not able to get what are > these column contains,I mean how to change it to the format in which I can > directly plot the data to get DCCM map... > For e.g in this form > Res1 Res2 Correlation coefficient > x yz > > On Sun, Jun 19, 2011 at 16:16, Tsjerk Wassenaar wrote: > > > Of course you did.. > --- > *Regards,* > Bipin Singh > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] cross correlations
Hi Bipin, You have three coordinates per residue, hence a 3Nx3N matrix. Cheers, Tsjerk On Jun 25, 2011 4:40 PM, "bipin singh" wrote: Hello, I have calculated the covariance matrix for C-alpha atoms(179 aa) only,but after plotting the correlation, I have observed that it is of 537X537,instead of179X179.Please suggest me how to get correlation between the C-alpha atoms only. On Fri, Jun 24, 2011 at 22:54, Tsjerk Wassenaar wrote: > > Hi Bipin, > > Read... -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] About the %SS values in the output of do_dssp
Dear All, I have simulated 6 peptides (with 7 AA each capped in N and C termini) in water and trehalose. During all the simulation time, the six peptides have b-sheet conformations. I would like to calculate the average % of secondary structure for the 6 peptides over the course of run. So I have read the subject reported in the following link http://redmine.gromacs.org/issues/683and used the following command for the two first frames /work/sa001/gmx-post4.5.3/bin/do_dssp_mpi -f *-Center_All.xtc -s run_1.tpr -tu ps -dt 1 -b 1 -e 5 -o 6_Peptide_53A6_Trehal_Pref_SS.xpm -sss 6_Peptide_53A6_Trehal_Pref_HEBT.dat -ssdump 6_Peptide_53A6_Trehal_Dump_SS.dat -sc test.xvg I obtained the following output for my six peptides @TYPE xy @ subtitle "Structure = + + + + + + + + + + + + + + + + + + + + + + + + + + + + B-Sheet + + + + + + " @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Structure" @ s1 legend "Coil" @ s2 legend "B-Sheet" @ s3 legend "Chain_Separator" 2301230 5 4301230 5 # Totals60246010 # SS %0.64 0.26 0.64 0.11 I can understand how the %SS values are obtained in the example given in http://redmine.gromacs.org/issues/683, but not in my case. Could you tell me how the %SS is obtained the output above. Thank you in advance for your help SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] About the %SS values in the output of do_dssp
sa wrote:
Dear All,
I have simulated 6 peptides (with 7 AA each capped in N and C termini)
in water and trehalose. During all the simulation time, the six peptides
have b-sheet conformations. I would like to calculate the average % of
secondary structure for the 6 peptides over the course of run. So I have
read the subject reported in the following link
http://redmine.gromacs.org/issues/683 and used the following command for
the two first frames
/work/sa001/gmx-post4.5.3/bin/do_dssp_mpi -f *-Center_All.xtc -s
run_1.tpr -tu ps -dt 1 -b 1 -e 5 -o
6_Peptide_53A6_Trehal_Pref_SS.xpm -sss
6_Peptide_53A6_Trehal_Pref_HEBT.dat -ssdump
6_Peptide_53A6_Trehal_Dump_SS.dat -sc test.xvg
I obtained the following output for my six peptides
@TYPE xy
@ subtitle "Structure = + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + B-Sheet + + + + + + "
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Structure"
@ s1 legend "Coil"
@ s2 legend "B-Sheet"
@ s3 legend "Chain_Separator"
2301230 5
4301230 5
# Totals60246010
# SS %0.64 0.26 0.64 0.11
I can understand how the %SS values are obtained in the example given in
http://redmine.gromacs.org/issues/683, but not in my case. Could you
tell me how the %SS is obtained the output above.
Like any other average. From the code:
/* now print percentages */
fprintf(fp, "%-8s %5.2f", "# SS %", total_count / (real) (mat->nx *
mat->ny));
for(s=0; snmap; s++)
{
fprintf(fp," %5.2f",total[s] / (real) (mat->nx * mat->ny));
}
fprintf(fp,"\n");
So the total number of secondary structure elements is divided by the product of
(number of frames * number of total residues).
Your results are affected by the problem I mentioned in the issue report you
quote. You have 42 residues, but since chain separators count as residues, the
calculations are all done out of 47 residues instead. You'll have to either
modify the code to account for this problem or simply re-calculate the averages
yourself.
-Justin
Thank you in advance for your help
SA
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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[gmx-users] Simulation of Primed DNA
Dear Experts, Hi from a beginner in Gromacs, I am trying to simulate i-motif so I have primed all the four chains and manually created a phosphodiester bond between two i-motif units. all the with Amber/Gromos ff the problem is : Fatal error: Atom P in residue DT 1 was not found in rtp entry DT5 with 30 atoms while sorting atoms. while Charmm36ff - Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. while it works well if I use non primed i-motif and only single unit. I am very new to gromacs and I have only done some simulations of Proteins. I am in serious trouble..help required at large scale :) Thank You All Raghav -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Simulation of Primed DNA
raghav singh wrote: Dear Experts, Hi from a beginner in Gromacs, I am trying to simulate i-motif so I have primed all the four chains and manually created a phosphodiester bond between two i-motif units. all the with Amber/Gromos ff the problem is : Fatal error: Atom P in residue DT 1 was not found in rtp entry DT5 with 30 atoms while sorting atoms. while Charmm36ff - Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. while it works well if I use non primed i-motif and only single unit. I am very new to gromacs and I have only done some simulations of Proteins. I am in serious trouble..help required at large scale :) Nearly all common error messages (including these) are explained on the Gromacs website: http://www.gromacs.org/Documentation/Errors In general, if there is no answer there, please search the list archives. Both of these errors come up very frequently, as will most that you will likely encounter. Note that in your case, pdb2gmx is going to have a hard time generating a topology, since in the i-motif there are numerous non-linear bonds. pdb2gmx is only particularly well-suited for linear molecules, with very limited support for branching. You will have to add entries in specbond.dat to create these branched bonds. See the manual for implementation details, as well as: http://www.gromacs.org/Documentation/File_Formats/specbond.dat -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Periodic Images - clarification
Dear users, I apologize for asking the same question. but I wanted a clarification regarding this I had done a simulation for 100ns which had minimum image violation after 27ns. I have asked this question several times and people have suggested me not to use the results. But I just wanted to know if I use the frames upto 26ns and do an analysis will it be wrong? and if I report that this minimum image violation had occurred. Correct me if I am wrong. This minimum image violation occurs only if the box size is inadequate. is it right? In the present simulation I had made sure that cut off (1.4nm) was much less than the periodic image distance 2.0nm. I may just ignore this data and do another simulation, But I wanted to know this aspect. Kindly suggest. Thank you With Regards M. Kavyashree -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] (no subject)
Hi, Upon running g_helix_d -s md.tpr -n md.ndx -f md.trr I got the following output: Fatal error: rnr==0. Please tell me how can I proceed? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
