Re: [gmx-users] Regarding xpm2ps
Hello, I am using the below .m2p file as input for xpm2ps, but not able to get axis range label. ; Matrix options titlefont = Helvetica ; Matrix title Postscript Font name titlefontsize = 20.0 ; Matrix title Font size (pt) legend = yes ; Show the legend legendfont = Helvetica ; Legend name Postscript Font name legendfontsize = 12.0 ; Legend name Font size (pt) legendlabel ; Used when there is none in the .xpm legend2label; Id. when merging two xpm's xbox= 0 ; x-size of a matrix element ybox= 0 ; y-size of a matrix element matrixspacing = 20.0 ; Space between 2 matrices xoffset = 0.0 ; Between matrix and bounding box yoffset = 0.0 ; Between matrix and bounding box ; X-axis options x-lineat0value = no; Draw line at matrix value==0 x-major = 4; Major tick spacing x-minor = 2 ; Id. Minor ticks x-firstmajor= 0 ; Offset for major tick x-majorat0 = no; Additional Major tick at first frame x-majorticklen = 8.0 ; Length of major ticks x-minorticklen = 4.0 ; Id. Minor ticks x-label = ; Used when there is none in the .xpm x-font = Helvetica ; Axis label PostScript Font x-fontsize = 12; Axis label Font size (pt) x-tickfont = Helvetica ; Tick label PostScript Font x-tickfontsize = 8 ; Tick label Font size (pt) ;Y-axis options y-lineat0value = no y-major = 4 y-minor = 2 y-firstmajor= 0 y-majorat0 = no y-majorticklen = 8.0 y-minorticklen = 4.0 y-label = y-fontsize = 12 y-font = Helvetica y-tickfontsize = 8 y-tickfont = Helvetica On Wed, Aug 24, 2011 at 00:52, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I have xpm matrix file, for converting this file to ps format I am using xpm2ps e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label mentioned for x and y-axis, in ps file.Please let me know how to set x and y axis range label in ps file. for example I want to set the x and y-axis range from -4 to +4. Use an .m2p file: http://manual.gromacs.org/online/m2p.html -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 list gmx-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
[gmx-users] error:You might need to add atom H to the hydrogen database of residue
Hi all, I am using Gromacs 4.0.5 with the forcefield amber03 in a red hat linux machine to simulate a protein-DNA complex. Eventhough I manually edited my pdb file to adhere to the amber nomenclature, I get the below error. I have not been able to pinpoint where in the pdb file, ffamber03.rtp, and ffamber03.hdbthe error could be -- if it's a nomenclature error. Would be great to receive some pointers on this. pdb2gmx -f prim_amb.pdb -o prim_amb.gro -water spc -ff amber03 . . . . . WARNING: atom H is missing in residue GLY 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLY in the file ff???.hdb (see the manual) - Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.C, line: 704 Fatal error: There were 1 missing atoms in molecule Protein_C, if you want to use this incomplete topology anyhow, use the option-missing. I get the error message complaining about a missing hydrogen in the first residue, no matter what that residue is --- sayfor instance even if I delete the first GLYresiduefrommy pdb file. krish -- 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] error:You might need to add atom H to the hydrogen database of residue
you may need to use -ignh option in pdb2gmx. Jianguo From: Kamesh Narasimhan g0701...@nus.edu.sg To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Wednesday, 24 August 2011 14:42:28 Subject: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Hi all, I am using Gromacs 4.0.5 with the forcefield amber03 in a red hat linux machine to simulate a protein-DNA complex. Eventhough I manually edited my pdb file to adhere to the amber nomenclature, I get the below error. I have not been able to pinpoint where in the pdb file, ffamber03.rtp, and ffamber03.hdb the error could be -- if it's a nomenclature error. Would be great to receive some pointers on this. pdb2gmx -f prim_amb.pdb -o prim_amb.gro -water spc -ff amber03 . . . . . WARNING: atom H is missing in residue GLY 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLY in the file ff???.hdb (see the manual) - Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.C, line: 704 Fatal error: There were 1 missing atoms in molecule Protein_C, if you want to use this incomplete topology anyhow, use the option-missing. I get the error message complaining about a missing hydrogen in the first residue, no matter what that residue is --- say for instance even if I delete the first GLY residue from my pdb file. krish-- 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] error:You might need to add atom H to the hydrogen database of residue
Thanks Jianguo, It doesn't seem to make a difference even if i use -ignh -- I still get the same error. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Jianguo Li [ljg...@yahoo.com.sg] Sent: Wednesday, August 24, 2011 3:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue you may need to use -ignh option in pdb2gmx. Jianguo From: Kamesh Narasimhan g0701...@nus.edu.sg To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Wednesday, 24 August 2011 14:42:28 Subject: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Hi all, I am using Gromacs 4.0.5 with the forcefield amber03 in a red hat linux machine to simulate a protein-DNA complex. Eventhough I manually edited my pdb file to adhere to the amber nomenclature, I get the below error. I have not been able to pinpoint where in the pdb file, ffamber03.rtp, and ffamber03.hdbthe error could be -- if it's a nomenclature error. Would be great to receive some pointers on this. pdb2gmx -f prim_amb.pdb -o prim_amb.gro -water spc -ff amber03 . . . . . WARNING: atom H is missing in residue GLY 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLY in the file ff???.hdb (see the manual) - Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.C, line: 704 Fatal error: There were 1 missing atoms in molecule Protein_C, if you want to use this incomplete topology anyhow, use the option-missing. I get the error message complaining about a missing hydrogen in the first residue, no matter what that residue is --- sayfor instance even if I delete the first GLYresiduefrommy pdb file. krish -- 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] error:You might need to add atom H to the hydrogen database of residue
Not sure what is the problem. but if you have changed the name of the first/last residue as NXXX/CXXX, you may try to add these two names (NXXX and CXXX) to aminoacids.dat file (also change the number in the first line). Cheers, Jianguo From: Kamesh Narasimhan g0701...@nus.edu.sg To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 24 August 2011 15:10:13 Subject: RE: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Thanks Jianguo, It doesn't seem to make a difference even if i use -ignh -- I still get the same error. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Jianguo Li [ljg...@yahoo.com.sg] Sent: Wednesday, August 24, 2011 3:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue you may need to use -ignh option in pdb2gmx. Jianguo From: Kamesh Narasimhan g0701...@nus.edu.sg To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Wednesday, 24 August 2011 14:42:28 Subject: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Hi all, I am using Gromacs 4.0.5 with the forcefield amber03 in a red hat linux machine to simulate a protein-DNA complex. Eventhough I manually edited my pdb file to adhere to the amber nomenclature, I get the below error. I have not been able to pinpoint where in the pdb file, ffamber03.rtp, and ffamber03.hdb the error could be -- if it's a nomenclature error. Would be great to receive some pointers on this. pdb2gmx -f prim_amb.pdb -o prim_amb.gro -water spc -ff amber03 . . . . . WARNING: atom H is missing in residue GLY 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLY in the file ff???.hdb (see the manual) - Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.C, line: 704 Fatal error: There were 1 missing atoms in molecule Protein_C, if you want to use this incomplete topology anyhow, use the option-missing. I get the error message complaining about a missing hydrogen in the first residue, no matter what that residue is --- say for instance even if I delete the first GLY residue from my pdb file. krish-- 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] error:You might need to add atom H to the hydrogen database of residue
The termini were changed to NXXX/CXXX and the aminoacids.dat file has these two names as well. So nothing very evident. I can see that there was a thread on precisely this issue --- but how it was resolved is not very evident. http://www.mail-archive.com/gmx-users@gromacs.org/msg18545.html From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Jianguo Li [ljg...@yahoo.com.sg] Sent: Wednesday, August 24, 2011 3:46 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Not sure what is the problem. but if you have changed the name of the first/last residue as NXXX/CXXX, you may try to add these two names (NXXX and CXXX) to aminoacids.dat file (also change the number in the first line). Cheers, Jianguo From: Kamesh Narasimhan g0701...@nus.edu.sg To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 24 August 2011 15:10:13 Subject: RE: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Thanks Jianguo, It doesn't seem to make a difference even if i use -ignh -- I still get the same error. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Jianguo Li [ljg...@yahoo.com.sg] Sent: Wednesday, August 24, 2011 3:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue you may need to use -ignh option in pdb2gmx. Jianguo From: Kamesh Narasimhan g0701...@nus.edu.sg To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Wednesday, 24 August 2011 14:42:28 Subject: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Hi all, I am using Gromacs 4.0.5 with the forcefield amber03 in a red hat linux machine to simulate a protein-DNA complex. Eventhough I manually edited my pdb file to adhere to the amber nomenclature, I get the below error. I have not been able to pinpoint where in the pdb file, ffamber03.rtp, and ffamber03.hdbthe error could be -- if it's a nomenclature error. Would be great to receive some pointers on this. pdb2gmx -f prim_amb.pdb -o prim_amb.gro -water spc -ff amber03 . . . . . WARNING: atom H is missing in residue GLY 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLY in the file ff???.hdb (see the manual) - Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.C, line: 704 Fatal error: There were 1 missing atoms in molecule Protein_C, if you want to use this incomplete topology anyhow, use the option-missing. I get the error message complaining about a missing hydrogen in the first residue, no matter what that residue is --- sayfor instance even if I delete the first GLYresiduefrommy pdb file. krish -- 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] Regarding xpm2ps
bipin singh wrote: Hello, I am using the below .m2p file as input for xpm2ps, but not able to get axis range label. What axis range do you obtain? If your data do not actually span from -4 to 4, there's not much you can do. I was assuming you had data that did fit this range. You also didn't say which tool produced the .xpm file; some programs can be forced to adjust the data range, but others can't. -Justin ; Matrix options titlefont = Helvetica ; Matrix title Postscript Font name titlefontsize = 20.0 ; Matrix title Font size (pt) legend = yes ; Show the legend legendfont = Helvetica ; Legend name Postscript Font name legendfontsize = 12.0 ; Legend name Font size (pt) legendlabel ; Used when there is none in the .xpm legend2label; Id. when merging two xpm's xbox= 0 ; x-size of a matrix element ybox= 0 ; y-size of a matrix element matrixspacing = 20.0 ; Space between 2 matrices xoffset = 0.0 ; Between matrix and bounding box yoffset = 0.0 ; Between matrix and bounding box ; X-axis options x-lineat0value = no; Draw line at matrix value==0 x-major = 4; Major tick spacing x-minor = 2 ; Id. Minor ticks x-firstmajor= 0 ; Offset for major tick x-majorat0 = no; Additional Major tick at first frame x-majorticklen = 8.0 ; Length of major ticks x-minorticklen = 4.0 ; Id. Minor ticks x-label = ; Used when there is none in the .xpm x-font = Helvetica ; Axis label PostScript Font x-fontsize = 12; Axis label Font size (pt) x-tickfont = Helvetica ; Tick label PostScript Font x-tickfontsize = 8 ; Tick label Font size (pt) ;Y-axis options y-lineat0value = no y-major = 4 y-minor = 2 y-firstmajor= 0 y-majorat0 = no y-majorticklen = 8.0 y-minorticklen = 4.0 y-label = y-fontsize = 12 y-font = Helvetica y-tickfontsize = 8 y-tickfont = Helvetica On Wed, Aug 24, 2011 at 00:52, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I have xpm matrix file, for converting this file to ps format I am using xpm2ps e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label mentioned for x and y-axis, in ps file.Please let me know how to set x and y axis range label in ps file. for example I want to set the x and y-axis range from -4 to +4. Use an .m2p file: http://manual.gromacs.org/online/m2p.html -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 -- 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
Re: [gmx-users] Regarding xpm2ps
Thanks for your reply, I am attaching the xpm file which I got from g_sham and also attaching the eps output got from xpm2ps.As you can see there is no axis range(PC1 and PC2) labeled in eps file. As the PC1 range is from -4 to +4 and PC2 range from -5 to +4, I want the x-axis range in eps file from -4 to +4(PC1) and y-axis range from -5 to +4(PC2) regardless of the data values in xpm file. But I am unable to get using .m2p file. On Wed, Aug 24, 2011 at 16:22, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I am using the below .m2p file as input for xpm2ps, but not able to get axis range label. What axis range do you obtain? If your data do not actually span from -4 to 4, there's not much you can do. I was assuming you had data that did fit this range. You also didn't say which tool produced the .xpm file; some programs can be forced to adjust the data range, but others can't. -Justin ; Matrix options titlefont = Helvetica ; Matrix title Postscript Font name titlefontsize = 20.0 ; Matrix title Font size (pt) legend = yes ; Show the legend legendfont = Helvetica ; Legend name Postscript Font name legendfontsize = 12.0 ; Legend name Font size (pt) legendlabel ; Used when there is none in the .xpm legend2label ; Id. when merging two xpm's xbox = 0 ; x-size of a matrix element ybox = 0 ; y-size of a matrix element matrixspacing = 20.0 ; Space between 2 matrices xoffset = 0.0 ; Between matrix and bounding box yoffset = 0.0 ; Between matrix and bounding box ; X-axis options x-lineat0value = no ; Draw line at matrix value==0 x-major = 4 ; Major tick spacing x-minor = 2 ; Id. Minor ticks x-firstmajor = 0 ; Offset for major tick x-majorat0 = no ; Additional Major tick at first frame x-majorticklen = 8.0 ; Length of major ticks x-minorticklen = 4.0 ; Id. Minor ticks x-label = ; Used when there is none in the .xpm x-font = Helvetica ; Axis label PostScript Font x-fontsize = 12 ; Axis label Font size (pt) x-tickfont = Helvetica ; Tick label PostScript Font x-tickfontsize = 8 ; Tick label Font size (pt) ;Y-axis options y-lineat0value = no y-major = 4 y-minor = 2 y-firstmajor = 0 y-majorat0 = no y-majorticklen = 8.0 y-minorticklen = 4.0 y-label = y-fontsize = 12 y-font = Helvetica y-tickfontsize = 8 y-tickfont = Helvetica On Wed, Aug 24, 2011 at 00:52, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I have xpm matrix file, for converting this file to ps format I am using xpm2ps e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label mentioned for x and y-axis, in ps file.Please let me know how to set x and y axis range label in ps file. for example I want to set the x and y-axis range from -4 to +4. Use an .m2p file: http://manual.gromacs.org/online/m2p.html -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 list gmx-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 -- 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 list gmx-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 attachment: gibbs.xpm gibbs.eps Description: PostScript document -- 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
Re: [gmx-users] Regarding xpm2ps
bipin singh wrote: Thanks for your reply, I am attaching the xpm file which I got from g_sham and also attaching the eps output got from xpm2ps.As you can see there is no axis range(PC1 and PC2) labeled in eps file. As the PC1 range is from -4 to +4 and PC2 range from -5 to +4, I want the x-axis range in eps file from -4 to +4(PC1) and y-axis range from -5 to +4(PC2) regardless of the data values in xpm file. But I am unable to get using .m2p file. The .m2p file can only be used to adjust axes if the data fit the range you want already. This was unclear from your earlier post. Now that you've said what program you used, we can solve this. g_sham allows you to set the axis manually with the -xmin and -xmax options. Re-run g_sham with these options to set the axes and you should have no problem. -Justin On Wed, Aug 24, 2011 at 16:22, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I am using the below .m2p file as input for xpm2ps, but not able to get axis range label. What axis range do you obtain? If your data do not actually span from -4 to 4, there's not much you can do. I was assuming you had data that did fit this range. You also didn't say which tool produced the .xpm file; some programs can be forced to adjust the data range, but others can't. -Justin ; Matrix options titlefont = Helvetica ; Matrix title Postscript Font name titlefontsize = 20.0 ; Matrix title Font size (pt) legend = yes ; Show the legend legendfont = Helvetica ; Legend name Postscript Font name legendfontsize = 12.0 ; Legend name Font size (pt) legendlabel ; Used when there is none in the .xpm legend2label; Id. when merging two xpm's xbox= 0 ; x-size of a matrix element ybox= 0 ; y-size of a matrix element matrixspacing = 20.0 ; Space between 2 matrices xoffset = 0.0 ; Between matrix and bounding box yoffset = 0.0 ; Between matrix and bounding box ; X-axis options x-lineat0value = no; Draw line at matrix value==0 x-major = 4; Major tick spacing x-minor = 2 ; Id. Minor ticks x-firstmajor= 0 ; Offset for major tick x-majorat0 = no; Additional Major tick at first frame x-majorticklen = 8.0 ; Length of major ticks x-minorticklen = 4.0 ; Id. Minor ticks x-label = ; Used when there is none in the .xpm x-font = Helvetica ; Axis label PostScript Font x-fontsize = 12; Axis label Font size (pt) x-tickfont = Helvetica ; Tick label PostScript Font x-tickfontsize = 8 ; Tick label Font size (pt) ;Y-axis options y-lineat0value = no y-major = 4 y-minor = 2 y-firstmajor= 0 y-majorat0 = no y-majorticklen = 8.0 y-minorticklen = 4.0 y-label = y-fontsize = 12 y-font = Helvetica y-tickfontsize = 8 y-tickfont = Helvetica On Wed, Aug 24, 2011 at 00:52, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I have xpm matrix file, for converting this file to ps format I am using xpm2ps e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label mentioned for x and y-axis, in ps file.Please let me know how to set x and y axis range label in ps file. for example I want to set the x and y-axis range from -4 to +4. Use an .m2p file: http://manual.gromacs.org/online/m2p.html -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 -- 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] Conversion of gromacs trajectory file
Hello Everyone, Any idea how one can convert gromacs trajectory file to amber file. So as to use the amber tools. Thank you, Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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] Conversion of gromacs trajectory file
aiswarya.pa...@gmail.com wrote: Hello Everyone, Any idea how one can convert gromacs trajectory file to amber file. So as to use the amber tools. The key is finding a compatible intermediate that can be converted. I've found that PDB format is pretty universal. I have a script that does the opposite (mdcrd to .xtc) linked from my site: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html It's a bit awkward, but does the job. Perhaps you can reverse-engineer it for your purpose. -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
Re: [gmx-users] Conversion of gromacs trajectory file
Hi Justin, Thank for the quick response. I would try out your script for the conversion. Best, Aiswarya --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Discussion list for GROMACS users ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Conversion of gromacs trajectory file Sent: 24 Aug 2011 5:35 PM aiswarya.pa...@gmail.com wrote: Hello Everyone, Any idea how one can convert gromacs trajectory file to amber file. So as to use the amber tools. The key is finding a compatible intermediate that can be converted. I've found that PDB format is pretty universal. I have a script that does the opposite (mdcrd to .xtc) linked from my site: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html It's a bit awkward, but does the job. Perhaps you can reverse-engineer it for your purpose. -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 Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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] Hydrogen existence time
Dear all, Does Hydrogen bond existence in a time frame states the residence time of the water molecule? Thank you, Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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] Hydrogen existence time
aiswarya.pa...@gmail.com wrote: Dear all, Does Hydrogen bond existence in a time frame states the residence time of the water molecule? Not necessarily, no. -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] Convert drug Charmm topology to Gromacs
Dear Gromacs Users, I have generated topology file for CHARMM ff using online server for my small molecule (I obtained .str file). How can I convert it into the Gromacs topology file (.itp)? Thanks, Steve -- 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] Hydrogen existence time
Dear Justin, So what does the hydrogen bond existence state? Thanks --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Gromacs mail ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 5:54 PM aiswarya.pa...@gmail.com wrote: Dear all, Does Hydrogen bond existence in a time frame states the residence time of the water molecule? Not necessarily, no. -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 Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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] Convert drug Charmm topology to Gromacs
Steven Neumann wrote: Dear Gromacs Users, I have generated topology file for CHARMM ff using online server for my small molecule (I obtained .str file). How can I convert it into the Gromacs topology file (.itp)? Start with Chapter 5 of the manual to understand the required file format and contents, and then use the scripting language of your choice to extract the corresponding information. -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
Re: [gmx-users] Hydrogen existence time
aiswarya.pa...@gmail.com wrote: Dear Justin, So what does the hydrogen bond existence state? The length of time for which a given hydrogen bond exists (i.e. satisfies the geometrical criteria in the context of some particular partner group). -Justin Thanks --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Gromacs mail ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 5:54 PM aiswarya.pa...@gmail.com wrote: Dear all, Does Hydrogen bond existence in a time frame states the residence time of the water molecule? Not necessarily, no. -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
Re: [gmx-users] Hydrogen existence time
Any idea how can I calculate the residence time of water. Aiswarya --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Gromacs mail ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 5:58 PM aiswarya.pa...@gmail.com wrote: Dear Justin, So what does the hydrogen bond existence state? The length of time for which a given hydrogen bond exists (i.e. satisfies the geometrical criteria in the context of some particular partner group). -Justin Thanks --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Gromacs mail ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 5:54 PM aiswarya.pa...@gmail.com wrote: Dear all, Does Hydrogen bond existence in a time frame states the residence time of the water molecule? Not necessarily, no. -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 Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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] Convert drug Charmm topology to Gromacs
On 24/08/2011 10:27 PM, Justin A. Lemkul wrote: Steven Neumann wrote: Dear Gromacs Users, I have generated topology file for CHARMM ff using online server for my small molecule (I obtained .str file). How can I convert it into the Gromacs topology file (.itp)? Start with Chapter 5 of the manual to understand the required file format and contents, and then use the scripting language of your choice to extract the corresponding information. -Justin Or use SwissParam to generate in the GROMACS format the first time. 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/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] Regarding xpm2ps
Thanks for your kind help, I have tried as per your suggestion, the below command g_sham -f 2d_proj.xvg -xmin -5 -xmax 5 -ls gibbs.xpm It is running without any error , but it is not giving any xpm output... On Wed, Aug 24, 2011 at 17:18, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your reply, I am attaching the xpm file which I got from g_sham and also attaching the eps output got from xpm2ps.As you can see there is no axis range(PC1 and PC2) labeled in eps file. As the PC1 range is from -4 to +4 and PC2 range from -5 to +4, I want the x-axis range in eps file from -4 to +4(PC1) and y-axis range from -5 to +4(PC2) regardless of the data values in xpm file. But I am unable to get using .m2p file. The .m2p file can only be used to adjust axes if the data fit the range you want already. This was unclear from your earlier post. Now that you've said what program you used, we can solve this. g_sham allows you to set the axis manually with the -xmin and -xmax options. Re-run g_sham with these options to set the axes and you should have no problem. -Justin On Wed, Aug 24, 2011 at 16:22, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I am using the below .m2p file as input for xpm2ps, but not able to get axis range label. What axis range do you obtain? If your data do not actually span from -4 to 4, there's not much you can do. I was assuming you had data that did fit this range. You also didn't say which tool produced the .xpm file; some programs can be forced to adjust the data range, but others can't. -Justin ; Matrix options titlefont = Helvetica ; Matrix title Postscript Font name titlefontsize = 20.0 ; Matrix title Font size (pt) legend = yes ; Show the legend legendfont = Helvetica ; Legend name Postscript Font name legendfontsize = 12.0 ; Legend name Font size (pt) legendlabel ; Used when there is none in the .xpm legend2label ; Id. when merging two xpm's xbox = 0 ; x-size of a matrix element ybox = 0 ; y-size of a matrix element matrixspacing = 20.0 ; Space between 2 matrices xoffset = 0.0 ; Between matrix and bounding box yoffset = 0.0 ; Between matrix and bounding box ; X-axis options x-lineat0value = no ; Draw line at matrix value==0 x-major = 4 ; Major tick spacing x-minor = 2 ; Id. Minor ticks x-firstmajor = 0 ; Offset for major tick x-majorat0 = no ; Additional Major tick at first frame x-majorticklen = 8.0 ; Length of major ticks x-minorticklen = 4.0 ; Id. Minor ticks x-label = ; Used when there is none in the .xpm x-font = Helvetica ; Axis label PostScript Font x-fontsize = 12 ; Axis label Font size (pt) x-tickfont = Helvetica ; Tick label PostScript Font x-tickfontsize = 8 ; Tick label Font size (pt) ;Y-axis options y-lineat0value = no y-major = 4 y-minor = 2 y-firstmajor = 0 y-majorat0 = no y-majorticklen = 8.0 y-minorticklen = 4.0 y-label = y-fontsize = 12 y-font = Helvetica y-tickfontsize = 8 y-tickfont = Helvetica On Wed, Aug 24, 2011 at 00:52, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I have xpm matrix file, for converting this file to ps format I am using xpm2ps e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label mentioned for x and y-axis, in ps file.Please let me know how to set x and y axis range label in ps file. for example I want to set the x and y-axis range from -4 to +4. Use an .m2p file: http://manual.gromacs.org/online/m2p.html -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 list gmx-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 -- 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
Re: [gmx-users] Hydrogen existence time
aiswarya.pa...@gmail.com wrote: Any idea how can I calculate the residence time of water. There have been recent discussions on this topic, so please check the archive. The solution is an external program that one of the users provided; there are no Gromacs tools that will do this. -Justin Aiswarya --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Gromacs mail ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 5:58 PM aiswarya.pa...@gmail.com wrote: Dear Justin, So what does the hydrogen bond existence state? The length of time for which a given hydrogen bond exists (i.e. satisfies the geometrical criteria in the context of some particular partner group). -Justin Thanks --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Gromacs mail ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 5:54 PM aiswarya.pa...@gmail.com wrote: Dear all, Does Hydrogen bond existence in a time frame states the residence time of the water molecule? Not necessarily, no. -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
Re: [gmx-users] Regarding xpm2ps
bipin singh wrote: Thanks for your kind help, I have tried as per your suggestion, the below command g_sham -f 2d_proj.xvg -xmin -5 -xmax 5 -ls gibbs.xpm It is running without any error , but it is not giving any xpm output... Try with -xmin -5 -5 0 -xmax 5 5 0 - the meaning of the z-axis quantities here has never been clear to me since -gmax should control the range of z-values. Leaving them at zero should cause g_sham to calculate the appropriate range. Otherwise, you're limited to values of z between -5 and 5 also, which may not be appropriate. -Justin On Wed, Aug 24, 2011 at 17:18, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your reply, I am attaching the xpm file which I got from g_sham and also attaching the eps output got from xpm2ps.As you can see there is no axis range(PC1 and PC2) labeled in eps file. As the PC1 range is from -4 to +4 and PC2 range from -5 to +4, I want the x-axis range in eps file from -4 to +4(PC1) and y-axis range from -5 to +4(PC2) regardless of the data values in xpm file. But I am unable to get using .m2p file. The .m2p file can only be used to adjust axes if the data fit the range you want already. This was unclear from your earlier post. Now that you've said what program you used, we can solve this. g_sham allows you to set the axis manually with the -xmin and -xmax options. Re-run g_sham with these options to set the axes and you should have no problem. -Justin On Wed, Aug 24, 2011 at 16:22, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I am using the below .m2p file as input for xpm2ps, but not able to get axis range label. What axis range do you obtain? If your data do not actually span from -4 to 4, there's not much you can do. I was assuming you had data that did fit this range. You also didn't say which tool produced the .xpm file; some programs can be forced to adjust the data range, but others can't. -Justin ; Matrix options titlefont = Helvetica ; Matrix title Postscript Font name titlefontsize = 20.0 ; Matrix title Font size (pt) legend = yes ; Show the legend legendfont = Helvetica ; Legend name Postscript Font name legendfontsize = 12.0 ; Legend name Font size (pt) legendlabel ; Used when there is none in the .xpm legend2label; Id. when merging two xpm's xbox= 0 ; x-size of a matrix element ybox= 0 ; y-size of a matrix element matrixspacing = 20.0 ; Space between 2 matrices xoffset = 0.0 ; Between matrix and bounding box yoffset = 0.0 ; Between matrix and bounding box ; X-axis options x-lineat0value = no; Draw line at matrix value==0 x-major = 4; Major tick spacing x-minor = 2 ; Id. Minor ticks x-firstmajor= 0 ; Offset for major tick x-majorat0 = no; Additional Major tick at first frame x-majorticklen = 8.0 ; Length of major ticks x-minorticklen = 4.0 ; Id. Minor ticks x-label = ; Used when there is none in the .xpm x-font = Helvetica ; Axis label PostScript Font x-fontsize = 12; Axis label Font size (pt) x-tickfont = Helvetica ; Tick label PostScript Font x-tickfontsize = 8 ; Tick label Font size (pt) ;Y-axis options y-lineat0value = no y-major = 4 y-minor = 2 y-firstmajor= 0 y-majorat0 = no y-majorticklen = 8.0 y-minorticklen = 4.0 y-label = y-fontsize = 12 y-font = Helvetica y-tickfontsize = 8 y-tickfont = Helvetica On Wed, Aug 24, 2011 at 00:52, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I have xpm matrix file, for converting this file to ps format I am using xpm2ps e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label mentioned for x and y-axis, in ps file.Please let me know how to set x and y axis range label in ps file. for example I want to set the x and y-axis range from -4 to +4. Use an .m2p file: http://manual.gromacs.org/online/m2p.html -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 -- Justin A. Lemkul Ph.D.
Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue
It's reading it as GLY tho so maybe you have NGLY in the wrong column? Maybe try move it over one to the right? Oliver On 24 August 2011 09:47, Kamesh Narasimhan g0701...@nus.edu.sg wrote: The termini were changed to NXXX/CXXX and the aminoacids.dat file has these two names as well. So nothing very evident. I can see that there was a thread on precisely this issue --- but how it was resolved is not very evident. http://www.mail-archive.com/gmx-users@gromacs.org/msg18545.html -- *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Jianguo Li [ljg...@yahoo.com.sg] *Sent:* Wednesday, August 24, 2011 3:46 PM *To:* Discussion list for GROMACS users *Subject:* Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Not sure what is the problem. but if you have changed the name of the first/last residue as NXXX/CXXX, you may try to add these two names (NXXX and CXXX) to aminoacids.dat file (also change the number in the first line). Cheers, Jianguo -- *From:* Kamesh Narasimhan g0701...@nus.edu.sg *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, 24 August 2011 15:10:13 *Subject:* RE: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Thanks Jianguo, It doesn't seem to make a difference even if i use -ignh -- I still get the same error. -- *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Jianguo Li [ljg...@yahoo.com.sg] *Sent:* Wednesday, August 24, 2011 3:06 PM *To:* Discussion list for GROMACS users *Subject:* Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue you may need to use -ignh option in pdb2gmx. Jianguo -- *From:* Kamesh Narasimhan g0701...@nus.edu.sg *To:* gmx-users@gromacs.org gmx-users@gromacs.org *Sent:* Wednesday, 24 August 2011 14:42:28 *Subject:* [gmx-users] error:You might need to add atom H to the hydrogen database of residue Hi all, I am using Gromacs 4.0.5 with the forcefield amber03 in a red hat linux machine to simulate a protein-DNA complex. Eventhough I manually edited my pdb file to adhere to the amber nomenclature, I get the below error. I have not been able to pinpoint where in the pdb file, ffamber03.rtp, and ffamber03.hdb the error could be -- if it's a nomenclature error. Would be great to receive some pointers on this. pdb2gmx -f prim_amb.pdb -o prim_amb.gro -water spc -ff amber03 . . . . . WARNING: atom H is missing in residue GLY 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLY in the file ff???.hdb (see the manual) - Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.C, line: 704 Fatal error: There were 1 missing atoms in molecule Protein_C, if you want to use this incomplete topology anyhow, use the option-missing. I get the error message complaining about a missing hydrogen in the first residue, no matter what that residue is --- say for instance even if I delete the first GLY residue from my pdb file. krish -- 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
RE: [gmx-users] error:You might need to add atom H to the hydrogen database of residue
Thanks! that did it. It was the wrong column issue. However, I can see now thatI am getting a non-integer charge for my first nucleic acid chain using the amber03 forcefield. I did replace the aminoacids.dat with the aminoacids-NA.dat contents from the amber port. How do I overcome this ? From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Oliver Grant [olivercgr...@gmail.com] Sent: Wednesday, August 24, 2011 9:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue It's reading it as GLY tho so maybe you have NGLY in the wrong column? Maybe try move it over one to the right? Oliver On 24 August 2011 09:47, Kamesh Narasimhan g0701...@nus.edu.sg wrote: The termini were changed to NXXX/CXXX and the aminoacids.dat file has these two names as well. So nothing very evident. I can see that there was a thread on precisely this issue --- but how it was resolved is not very evident. http://www.mail-archive.com/gmx-users@gromacs.org/msg18545.html From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Jianguo Li [ljg...@yahoo.com.sg] Sent: Wednesday, August 24, 2011 3:46 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Not sure what is the problem. but if you have changed the name of the first/last residue as NXXX/CXXX, you may try to add these two names (NXXX and CXXX) to aminoacids.dat file (also change the number in the first line). Cheers, Jianguo From: Kamesh Narasimhan g0701...@nus.edu.sg To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 24 August 2011 15:10:13 Subject: RE: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Thanks Jianguo, It doesn't seem to make a difference even if i use -ignh -- I still get the same error. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Jianguo Li [ljg...@yahoo.com.sg] Sent: Wednesday, August 24, 2011 3:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue you may need to use -ignh option in pdb2gmx. Jianguo From: Kamesh Narasimhan g0701...@nus.edu.sg To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Wednesday, 24 August 2011 14:42:28 Subject: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Hi all, I am using Gromacs 4.0.5 with the forcefield amber03 in a red hat linux machine to simulate a protein-DNA complex. Eventhough I manually edited my pdb file to adhere to the amber nomenclature, I get the below error. I have not been able to pinpoint where in the pdb file, ffamber03.rtp, and ffamber03.hdbthe error could be -- if it's a nomenclature error. Would be great to receive some pointers on this. pdb2gmx -f prim_amb.pdb -o prim_amb.gro -water spc -ff amber03 . . . . . WARNING: atom H is missing in residue GLY 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLY in the file ff???.hdb (see the manual) - Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.C, line: 704 Fatal error: There were 1 missing atoms in molecule Protein_C, if you want to use this incomplete topology anyhow, use the option-missing. I get the error message complaining about a missing hydrogen in the first residue, no matter what that residue is --- sayfor instance even if I delete the first GLYresiduefrommy pdb file. krish -- gmx-users mailing list gmx-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
Antw: Re: [gmx-users] Hydrogen existence time
You do not know, what you are doing as I suppose. I suggested you already to calculate the H-bond correlation time, or the self-diffusion coefficient of this specific molecule. Justin A. Lemkul 24.08.11 15.04 Uhr aiswarya.pa...@gmail.com wrote: Any idea how can I calculate the residence time of water. There have been recent discussions on this topic, so please check the archive. The solution is an external program that one of the users provided; there are no Gromacs tools that will do this. -Justin Aiswarya --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Gromacs mail ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 5:58 PM aiswarya.pa...@gmail.com wrote: Dear Justin, So what does the hydrogen bond existence state? The length of time for which a given hydrogen bond exists (i.e. satisfies the geometrical criteria in the context of some particular partner group). -Justin Thanks --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Gromacs mail ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 5:54 PM aiswarya.pa...@gmail.com wrote: Dear all, Does Hydrogen bond existence in a time frame states the residence time of the water molecule? Not necessarily, no. -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 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: Antw: Re: [gmx-users] Hydrogen existence time
Dear Emanuel, Iam following what you have mentioned earlier. But as you said hydrogen bond correlation time gives the average hydrogen bond existence time. So I confused understanding whether an H Bond existence time would give me the residence time. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de Sender: gmx-users-boun...@gromacs.org Date: Wed, 24 Aug 2011 15:42:11 To: gmx-users@gromacs.org; jalem...@vt.edu Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Antw: Re: [gmx-users] Hydrogen existence time -- 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
Re: [gmx-users] Hydrogen existence time
Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t. Aiswarya --Original Message-- From: Mark Abraham To: Aiswarya Pawar Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 6:09 PM On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: Any idea how can I calculate the residence time of water. First, seek define what you mean to calculate. If you can't write an equation down for it, you can't calculate it. Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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
Antw: Re: [gmx-users] Hydrogen existence time
As I told you, you can calculate the self-diffusion coefficient by using g_msd. Following: Large diffusion-coeff. -- means : The residence time is low. Small diffusion-coeff. -- means : The residence time is large Mean-square-displacement means: Displacement of molecules per time. No displacement of molecule at all : if(msd == 0) means: Infinite residence time. So I say from my idiotic point of view: msd ~ residence time ( I still do not know what you mean with this because this is usually related to chemical reactors in engineering and NOT in protein simulation ) In your index-file you can index those molecules, which you need. Your equation does not make sense. 24.08.11 16.01 Uhr Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t. Aiswarya --Original Message-- From: Mark Abraham To: Aiswarya Pawar Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 6:09 PM On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: Any idea how can I calculate the residence time of water. First, seek define what you mean to calculate. If you can't write an equation down for it, you can't calculate it. Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- 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] Convert drug Charmm topology to Gromacs
Hi, The .str file contains the information of atomtype, bonds and improper dihedrals, so it is eneough to write a .rtp file. Then using pdb2gmx to generate the itp file. And you also need to add the missing parameters from CgenFF into the itp parameter files based on chapter 5, as Justin suggested. best regards, Jianguo From: Steven Neumann s.neuman...@gmail.com To: gmx-users@gromacs.org Sent: Wednesday, 24 August 2011 20:26:13 Subject: [gmx-users] Convert drug Charmm topology to Gromacs Dear Gromacs Users, I have generated topology file for CHARMM ff using online server for my small molecule (I obtained .str file). How can I convert it into the Gromacs topology file (.itp)? Thanks, Steve -- 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] Convert drug Charmm topology to Gromacs
Hi, Thank you for the information. Is it easier just to use SwissParam as mentioned and straight obtain itp file for my drug? Steve On Wed, Aug 24, 2011 at 3:57 PM, Jianguo Li ljg...@yahoo.com.sg wrote: Hi, The .str file contains the information of atomtype, bonds and improper dihedrals, so it is eneough to write a .rtp file. Then using pdb2gmx to generate the itp file. And you also need to add the missing parameters from CgenFF into the itp parameter files based on chapter 5, as Justin suggested. best regards, Jianguo -- *From:* Steven Neumann s.neuman...@gmail.com *To:* gmx-users@gromacs.org *Sent:* Wednesday, 24 August 2011 20:26:13 *Subject:* [gmx-users] Convert drug Charmm topology to Gromacs Dear Gromacs Users, I have generated topology file for CHARMM ff using online server for my small molecule (I obtained .str file). How can I convert it into the Gromacs topology file (.itp)? Thanks, Steve -- 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
Re: Antw: Re: [gmx-users] Hydrogen existence time
Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to small character missing when typing from phone. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de Date: Wed, 24 Aug 2011 16:16:37 To: aiswarya.pa...@gmail.com; gmx-users@gromacs.org Subject: Antw: Re: [gmx-users] Hydrogen existence time As I told you, you can calculate the self-diffusion coefficient by using g_msd. Following: Large diffusion-coeff. -- means : The residence time is low. Small diffusion-coeff. -- means : The residence time is large Mean-square-displacement means: Displacement of molecules per time. No displacement of molecule at all : if(msd == 0) means: Infinite residence time. So I say from my idiotic point of view: msd ~ residence time ( I still do not know what you mean with this because this is usually related to chemical reactors in engineering and NOT in protein simulation ) In your index-file you can index those molecules, which you need. Your equation does not make sense. 24.08.11 16.01 Uhr Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t. Aiswarya --Original Message-- From: Mark Abraham To: Aiswarya Pawar Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 6:09 PM On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: Any idea how can I calculate the residence time of water. First, seek define what you mean to calculate. If you can't write an equation down for it, you can't calculate it. Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- 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: Antw: Re: [gmx-users] Hydrogen existence time
Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to some character missing when typing from phone. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: aiswarya.pa...@gmail.com Date: Wed, 24 Aug 2011 16:13:05 To: Gromacs mailgmx-users@gromacs.org Reply-To: aiswarya.pa...@gmail.com Subject: Re: Antw: Re: [gmx-users] Hydrogen existence time Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to small character missing when typing from phone. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de Date: Wed, 24 Aug 2011 16:16:37 To: aiswarya.pa...@gmail.com; gmx-users@gromacs.org Subject: Antw: Re: [gmx-users] Hydrogen existence time As I told you, you can calculate the self-diffusion coefficient by using g_msd. Following: Large diffusion-coeff. -- means : The residence time is low. Small diffusion-coeff. -- means : The residence time is large Mean-square-displacement means: Displacement of molecules per time. No displacement of molecule at all : if(msd == 0) means: Infinite residence time. So I say from my idiotic point of view: msd ~ residence time ( I still do not know what you mean with this because this is usually related to chemical reactors in engineering and NOT in protein simulation ) In your index-file you can index those molecules, which you need. Your equation does not make sense. 24.08.11 16.01 Uhr Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t. Aiswarya --Original Message-- From: Mark Abraham To: Aiswarya Pawar Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 6:09 PM On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: Any idea how can I calculate the residence time of water. First, seek define what you mean to calculate. If you can't write an equation down for it, you can't calculate it. Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- 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] gromacs: sound wave in liquid?
Dear all, Sorry if my question sounds irrelevant but I am wondering to know if in gromacs there is any tool for studying properties like sound wave/acoustic wave (An acoustic wave is a pressure oscillation that travels through liquid, in a wave pattern)? I dont see such a tool in the manual but I thought maybe someone has an idea how to indirectly extract these information. Please let me know your ideas. Thank you all, Regards, J. -- 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
Antw: Re: Antw: Re: [gmx-users] Hydrogen existence time
Good luck 24.08.11 18.14 Uhr Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to some character missing when typing from phone. AiswaryaSent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! From: aiswarya.pa...@gmail.com Date: Wed, 24 Aug 2011 16:13:05 + To: Gromacs mail ReplyTo: aiswarya.pa...@gmail.com Subject: Re: Antw: Re: [gmx-users] Hydrogen existence time Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to small character missing when typing from phone. AiswaryaSent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! From: Emanuel Peter Date: Wed, 24 Aug 2011 16:16:37 +0200 To: ; Subject: Antw: Re: [gmx-users] Hydrogen existence time As I told you, you can calculate the self-diffusion coefficient by using g_msd. Following: Large diffusion-coeff. -- means : The residence time is low. Small diffusion-coeff. -- means : The residence time is large Mean-square-displacement means: Displacement of molecules per time. No displacement of molecule at all : if(msd == 0) means: Infinite residence time. So I say from my idiotic point of view: msd ~ residence time ( I still do not know what you mean with this because this is usually related to chemical reactors in engineering and NOT in protein simulation ) In your index-file you can index those molecules, which you need. Your equation does not make sense. 24.08.11 16.01 Uhr Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t. Aiswarya --Original Message-- From: Mark Abraham To: Aiswarya Pawar Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 6:09 PM On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: Any idea how can I calculate the residence time of water. First, seek define what you mean to calculate. If you can't write an equation down for it, you can't calculate it. Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- 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] Convert drug Charmm topology to Gromacs
Steven Neumann wrote: Hi, Thank you for the information. Is it easier just to use SwissParam as mentioned and straight obtain itp file for my drug? I'd say so. Otherwise you have to go through the trouble of converting it all into the proper format and units. Writing an .rtp entry is just as much work as writing an .itp file (more or less), and pdb2gmx really isn't meant for standalone molecules, because then you'll have to do a bit more (trivial) cleanup to make the resulting .top an .itp file. If you have the means to produce a reasonable .itp file directly, do so. -Justin Steve On Wed, Aug 24, 2011 at 3:57 PM, Jianguo Li ljg...@yahoo.com.sg mailto:ljg...@yahoo.com.sg wrote: Hi, The .str file contains the information of atomtype, bonds and improper dihedrals, so it is eneough to write a .rtp file. Then using pdb2gmx to generate the itp file. And you also need to add the missing parameters from CgenFF into the itp parameter files based on chapter 5, as Justin suggested. best regards, Jianguo *From:* Steven Neumann s.neuman...@gmail.com mailto:s.neuman...@gmail.com *To:* gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Wednesday, 24 August 2011 20:26:13 *Subject:* [gmx-users] Convert drug Charmm topology to Gromacs Dear Gromacs Users, I have generated topology file for CHARMM ff using online server for my small molecule (I obtained .str file). How can I convert it into the Gromacs topology file (.itp)? Thanks, Steve -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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
Re: [gmx-users] gromacs: sound wave in liquid?
On Wed, 2011-08-24 at 12:25 -0400, Juliette N. wrote: Dear all, Sorry if my question sounds irrelevant but I am wondering to know if in gromacs there is any tool for studying properties like sound wave/acoustic wave (An acoustic wave is a pressure oscillation that travels through liquid, in a wave pattern)? I dont see such a tool in the manual but I thought maybe someone has an idea how to indirectly extract these information. Please let me know your ideas. Hi, this sounds like a task for a Lattice-Boltzmann code, which is unfortunately not implemented in GROMACS. Moreover as I assume that Coulomb interactions are involved, you perhaps will also get into trouble with momentum conservation, which is hard to achieve with the analytical form of the present SPME. An alternative would be to use the Ewald summation, but this code just runs in serial and for studying sound waves, I assume you need a quite large system, rendering Ewald extremely expensive as it scales with N^(3/2) in the best case. /Flo Thank you all, Regards, J. -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- 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] Regarding xpm2ps
Sir, Thanks a lot for your help..Its working... On Wed, Aug 24, 2011 at 18:34, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your kind help, I have tried as per your suggestion, the below command g_sham -f 2d_proj.xvg -xmin -5 -xmax 5 -ls gibbs.xpm It is running without any error , but it is not giving any xpm output... Try with -xmin -5 -5 0 -xmax 5 5 0 - the meaning of the z-axis quantities here has never been clear to me since -gmax should control the range of z-values. Leaving them at zero should cause g_sham to calculate the appropriate range. Otherwise, you're limited to values of z between -5 and 5 also, which may not be appropriate. -Justin On Wed, Aug 24, 2011 at 17:18, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your reply, I am attaching the xpm file which I got from g_sham and also attaching the eps output got from xpm2ps.As you can see there is no axis range(PC1 and PC2) labeled in eps file. As the PC1 range is from -4 to +4 and PC2 range from -5 to +4, I want the x-axis range in eps file from -4 to +4(PC1) and y-axis range from -5 to +4(PC2) regardless of the data values in xpm file. But I am unable to get using .m2p file. The .m2p file can only be used to adjust axes if the data fit the range you want already. This was unclear from your earlier post. Now that you've said what program you used, we can solve this. g_sham allows you to set the axis manually with the -xmin and -xmax options. Re-run g_sham with these options to set the axes and you should have no problem. -Justin On Wed, Aug 24, 2011 at 16:22, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I am using the below .m2p file as input for xpm2ps, but not able to get axis range label. What axis range do you obtain? If your data do not actually span from -4 to 4, there's not much you can do. I was assuming you had data that did fit this range. You also didn't say which tool produced the .xpm file; some programs can be forced to adjust the data range, but others can't. -Justin ; Matrix options titlefont = Helvetica ; Matrix title Postscript Font name titlefontsize = 20.0 ; Matrix title Font size (pt) legend = yes ; Show the legend legendfont = Helvetica ; Legend name Postscript Font name legendfontsize = 12.0 ; Legend name Font size (pt) legendlabel ; Used when there is none in the .xpm legend2label ; Id. when merging two xpm's xbox = 0 ; x-size of a matrix element ybox = 0 ; y-size of a matrix element matrixspacing = 20.0 ; Space between 2 matrices xoffset = 0.0 ; Between matrix and bounding box yoffset = 0.0 ; Between matrix and bounding box ; X-axis options x-lineat0value = no ; Draw line at matrix value==0 x-major = 4 ; Major tick spacing x-minor = 2 ; Id. Minor ticks x-firstmajor = 0 ; Offset for major tick x-majorat0 = no ; Additional Major tick at first frame x-majorticklen = 8.0 ; Length of major ticks x-minorticklen = 4.0 ; Id. Minor ticks x-label = ; Used when there is none in the .xpm x-font = Helvetica ; Axis label PostScript Font x-fontsize = 12 ; Axis label Font size (pt) x-tickfont = Helvetica ; Tick label PostScript Font x-tickfontsize = 8 ; Tick label Font size (pt) ;Y-axis options y-lineat0value = no y-major = 4 y-minor = 2 y-firstmajor = 0 y-majorat0 = no y-majorticklen = 8.0 y-minorticklen = 4.0 y-label = y-fontsize = 12 y-font = Helvetica y-tickfontsize = 8 y-tickfont = Helvetica On Wed, Aug 24, 2011 at 00:52, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I have xpm matrix file, for converting this file to ps format I am using xpm2ps e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label mentioned for x and y-axis, in ps file.Please let me know how to set x and y axis range label in ps file. for example I want to set the x and y-axis range from -4 to +4. Use an .m2p file: http://manual.gromacs.org/online/m2p.html -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 list gmx-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
[gmx-users] Difficulty building a topology for a synthetic branched PEG-peptide molecule
Hi all, I am trying to build a topology for a synthetic molecule that consists of peptides connected by oligoethyleneglycol (I'll call it PEG) linkers terminated with an amine and a carboxylic acid: -NH2-CH2-[CH2-O-CH2]n-CH2-C(=O)- The system looks like this: N-(PEG)-C-N-(peptide2)-Lys(C-ter)-NZ-C-(PEG)-N So: * the C-terminus of a PEG linker is attached to the N terminus of the peptide * the terminal Lys on the peptide is attached to the C-terminus of a PEG linker I was able to successfully build a topology for this molecule by: * defining appropriate residues (for the PEG chains and the Lys with a PEG attached on the NZ) in a local copy of the forcefield file, adding the residues' topologies to aminoacids.rtp * using the specbond.dat file to define the bond between the NZ in the Lys and the PEG linker * adding the residues to residuetypes.dat with a Protein type * calling pdb2gmx with the -ter option to assign the protonation states Now, I need to extend the topology to a molecule like this one: N-(peptide1)-C-N-(PEG)-C-N-(peptide2)-Lys(C-ter)-NZ-C-(PEG)-N-C-(peptide3)-N The difficulty with this molecule is that it has 2 N-termini and a single C-terminus (in the Lys with the PEG attached to the NZ sidechain). pdb2gmx recognizes the whole molecule as a peptide, but treats the last residue as a C-terminus, when it actually is an N-terminus. I found in the description for specbond.dat (http://www.gromacs.org/Documentation/File_Formats/specbond.dat) that for a branched peptide the -chainsep option of pdb2gmx can be used, so I started to work on that. I split the molecules in 2 chains like this: N-(peptide1)-C-N-(PEG)-C-N-(peptide2)-Lys(C-ter)-NZ- || -C-(PEG)-N-C-(peptide3)-N I reversed the order of the residues in the second chain, so that the residues are in N-to-C order. With this, pdb2gmx recognizes the proper termini when called as: $ pdb2gmx -f substrate_edited-reversed.pdb -ter -chainsep interactive I tried setting the protonation of the termini as charged for the real termini and None for the artificial one (the one that should be handled by specbond.dat), but I get an error message: ---[pdb2gmx output]--- [...] Splitting PDB chains based on TER records or changing chain id. Merge chain ending with residue LYSS27 (chain id ' ', atom 71 NZ) with chain starting with residue GLU28 (chain id 'p', atom 308 OE2)? [n/y] n Merged 1 chains into one molecule definition There are 2 chains and 0 blocks of water and 47 residues with 303 atoms chain #res #atoms 1 ' '27198 2 'p'17105 [...] Identified residue ARG1 as a starting terminus. Identified residue LYSS27 as a ending terminus. 9 out of 9 lines of specbond.dat converted successfully Special Atom Distance matrix: PEA118 CG1125 LYSS27 NZ198 2.762 Select start terminus type for ARG-1 0: NH3+ 1: NH2 2: None 0 Start terminus ARG-1: NH3+ Select end terminus type for LYSS-27 0: COO- 1: COOH 2: None 0 End terminus LYSS-27: COO- [...] Identified residue GLU28 as a starting terminus. Identified residue PEA47 as a ending terminus. 9 out of 9 lines of specbond.dat converted successfully Select start terminus type for GLU-28 0: NH3+ 1: NH2 2: None 0 Start terminus GLU-28: NH3+ Select end terminus type for PEA-47 0: COO- 1: COOH 2: None 2 End terminus PEA-47: None [...] --- Program pdb2gmx, VERSION 4.5.4 Source code file: pdb2top.c, line: 1035 Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- ---[pdb2gmx output]--- I think that the problem might stem from the fact that the C-terminus in the second chain is not a real peptide; I changed residuetypes.dat to have the PEG residues as Other, which causes pdb2gmx to recognize the last aminoacid as a C-terminus, but treating it as None yields the same error. Unfortunately, there is nothing about this error in http://www.gromacs.org/Documentation/Errors . Any suggestions on how to make this work will be greatly appreciated! -- Pablo Englebienne, PhD Dept. of Biomedical Engineering Dept. of Chemistry and Chemical Engineering Institute for Complex Molecular Systems (ICMS) Eindhoven University of Technology, TU/e PO Box 513, HG -1.26 5600 MB Eindhoven, The Netherlands Tel +31 40 247 5349 -- 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] Convert drug Charmm topology to Gromacs
Hello Steven Neumann, I recently converted CGenFF parameters into files that are used by Gromacs. If this is what you need, shoot me an email and I can provide you with the data sets. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.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/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] gromacs: sound wave in liquid?
On Wed, 24 Aug 2011 12:25:51 -0400 Juliette N. joojoojo...@gmail.com wrote: Dear all, Sorry if my question sounds irrelevant but I am wondering to know if in gromacs there is any tool for studying properties like sound wave/acoustic wave (An acoustic wave is a pressure oscillation that travels through liquid, in a wave pattern)? I dont see such a tool in the manual but I thought maybe someone has an idea how to indirectly extract these information. Please let me know your ideas. Given that pressure is a bit badly defined in MD simulations, I'd be somewhat skeptical about this. Not to mention the time scales - in order to simulate a sound wave say, at 44 kHz, you'd need to get at least two periods in your simulations, i.e. 45 microseconds, which is a *long* time on the nuclear / MD timescale. -- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.leht...@helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland Jussi Lehtola, FM Tohtorikoulutettava jussi.leht...@helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto Työpuhelin: (0)9 191 50 632 -- 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] index file subgroups
Hello, I am trying to figure out how to plot or obtain the average values of Gyration radius from different subgroups of index file. index file prompts for a single group and I need to calculate the averages for all subgroup by hand. Is there any way to compute averages or plot all subgroups directly? g_polystat -f *.trr -s *.tpr -o *.xvg -n *.ndx -w Thanks, 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/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] index file subgroups
Elisabeth wrote: Hello, I am trying to figure out how to plot or obtain the average values of Gyration radius from different subgroups of index file. index file prompts for a single group and I need to calculate the averages for all subgroup by hand. Is there any way to compute averages or plot all subgroups directly? Write a loop to call g_gyrate for each group you wish to analyze. -Justin g_polystat -f *.trr -s *.tpr -o *.xvg -n *.ndx -w Thanks, Regards, -- 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] gd_29 or gd_41 ?
Hi, For a H-NL-CH1-CH2 (H1-N-CA-C) dihedral angle in a N-terminal MET, why would pdb2gmx automatically assign gd_29 ? In /gromos53a6.ff/ffbonded.itp, it appears: #define gd_29 0.000 3.77 3 ; -C,CHn,SI- 0.9 ; ... #define gd_41 0.000 3.77 6 ; -CHn-NT- 0.9 ; ... Thanks, Yun Shi -- 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] Re: gd_29 or gd_41 ?
similarly, why would CA-CB-CG-OD2/1 in ASP be gd_40 instead of gd_34 ? #define gd_34 0.000 5.92 3 ; -CHn,SI-CHn-1.4 ; ... #define gd_40 0.0001.0 6 ; -CHn-C,NR(ring), CR1- 0.24 ; Something wrong with my interpretation of the comments after each definition? Thanks, Yun Shi On Wed, Aug 24, 2011 at 3:00 PM, Yun Shi yunsh...@gmail.com wrote: Hi, For a H-NL-CH1-CH2 (H1-N-CA-C) dihedral angle in a N-terminal MET, why would pdb2gmx automatically assign gd_29 ? In /gromos53a6.ff/ffbonded.itp, it appears: #define gd_29 0.000 3.77 3 ; -C,CHn,SI- 0.9 ; ... #define gd_41 0.000 3.77 6 ; -CHn-NT- 0.9 ; ... Thanks, Yun Shi -- 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] sugar dihedral parameters
Hi, In the ATB-distributed 53a6_carbo_new.dat, there are more than one set of parameters specified for some dihedral angles. For example, O5-C5-C6-O6 has a 1-fold term as gd_5, and a 3-fold term gd_37; C3-C2-C1-O5 has a 2-fold term as gd_17, and a 3-fold term as gd_34. So which one should I use? Thanks, Yun Shi -- 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] gd_29 or gd_41 ?
Yun Shi wrote: Hi, For a H-NL-CH1-CH2 (H1-N-CA-C) dihedral angle in a N-terminal MET, why would pdb2gmx automatically assign gd_29 ? In /gromos53a6.ff/ffbonded.itp, it appears: #define gd_29 0.000 3.77 3 ; -C,CHn,SI- 0.9 ; The comment here is incomplete. See the 53a6 paper for a complete description. -Justin ... #define gd_41 0.000 3.77 6 ; -CHn-NT- 0.9 ; ... Thanks, Yun Shi -- 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
Re: [gmx-users] Re: gd_29 or gd_41 ?
Yun Shi wrote: similarly, why would CA-CB-CG-OD2/1 in ASP be gd_40 instead of gd_34 ? #define gd_34 0.000 5.92 3 ; -CHn,SI-CHn-1.4 ; ... #define gd_40 0.0001.0 6 ; -CHn-C,NR(ring), CR1- 0.24 ; Something wrong with my interpretation of the comments after each definition? No, but the comments are somewhat shorthand. There's nothing wrong here, either. CG is a planar carbon. CHn is a tetrahedral center. So even though CG is not of type CR1, the dihedral is still correct, geometrically speaking. -Justin Thanks, Yun Shi On Wed, Aug 24, 2011 at 3:00 PM, Yun Shi yunsh...@gmail.com mailto:yunsh...@gmail.com wrote: Hi, For a H-NL-CH1-CH2 (H1-N-CA-C) dihedral angle in a N-terminal MET, why would pdb2gmx automatically assign gd_29 ? In /gromos53a6.ff/ffbonded.itp, it appears: #define gd_29 0.000 3.77 3 ; -C,CHn,SI- 0.9 ; ... #define gd_41 0.000 3.77 6 ; -CHn-NT- 0.9 ; ... Thanks, Yun Shi -- 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
Re: [gmx-users] sugar dihedral parameters
Yun Shi wrote: Hi, In the ATB-distributed 53a6_carbo_new.dat, there are more than one set of parameters specified for some dihedral angles. For example, O5-C5-C6-O6 has a 1-fold term as gd_5, and a 3-fold term gd_37; C3-C2-C1-O5 has a 2-fold term as gd_17, and a 3-fold term as gd_34. So which one should I use? You don't choose; you use both. Dihedrals are additive, and some interactions require a more complex energy term. -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
Re: [gmx-users] Hydrogen existence time
On 25/08/2011 12:00 AM, aiswarya.pa...@gmail.com wrote: Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t. So that's the autocorrelation of the existence function. Now you need a geometric criterion for existence. Note that g_hbond with well-constructed groups will calculate the autocorrelation of the existence function for an H-bond. See g_hbond -h. g_dist, some scripting and g_analyse might be necessary for other criteria. Mark Aiswarya --Original Message-- From: Mark Abraham To: Aiswarya Pawar Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 6:09 PM On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: Any idea how can I calculate the residence time of water. First, seek define what you mean to calculate. If you can't write an equation down for it, you can't calculate it. Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- 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] surface area calculations for MARTINI
Hi, I'm trying to do some surface area calculations on MARTINI models using APBS, which requires supplying vdw radii via a pqr file. Given how MARTINI treats LJ interactions (0.47 nm radius for all particle types), how do I calculate reasonable effective vdw radii? Obviously the PC headgroup (NC3) will have a larger vdw radius than the PE headgroup (NH3), and g_sas seems to account for this (reported ASA for -NC3 group is always higher than for -NH3 group) but I can't figure out how. Indeed, using editconf -mead to produce a pqr file from a MARTINI structure shows 2.35 A as the vdw radius for all lipid groups, which I fear will cause inaccurate calculations in APBS. Has anyone had this problem before? Mike -- Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 (formerly Qiang Cui group, University of Wisconsin-Madison) -- 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
