[gmx-users] -ee option in the g_analyze

Dear all I want to know what is difference between -ee option in the g_analyze which gives error estimate using block averaging and usual standard deviation or variance? which of them have advantage? Any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lis

[gmx-users] Fatal error: Number of grid cells is zero. Probably the system and box collapsed.

Dear gromacs user I did simulation of carbon nanotube (one in center and 6 in the vicinity of that)|: every CNT have 120 atoms. 1) energy minimization 2) equilibration in NVT ensemble when I did equilibration in NPT ensemble, I encountered Fatal error: Number of grid cells is zero. Probably the

[gmx-users] %exist of hydrogen bonds + No -map specified!

Dear Justin I'm using your script for obtaining %exist of hydrogen bonds. When I use ./hb.pl structure.pdb -map hbmap.xpm -index hbond.ndx, I encountered with No -map specified! I noted to points being at the begining of script: # 1. coordinate file (for atom naming) - MUST be a .pdb file

[gmx-users] g_select vs trjorder

Dear Justin If I want to know residue number of water molecules being within x nm of protein, for each frame, which tool is the best for me? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/

[gmx-users] g_select vs trjorder

Dear Justin You are wright. The two output files should not be equivalent. If I want to know residue number of water molecules being within x nm of protein, which tool is the best for me? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Pleas

[gmx-users] g_select vs trjorder

Dear Justin Thanks for your reply. I know, with g_select, I obtain index groups that tell me which atoms satisfy the given criteria and with trjorder, the coordinates of those atoms are reordered such that they are listed in sequence in the new trajectory. But g_select gives an output file (size

[gmx-users] g_select vs trjorder

Dear all Which one of g_select and trjorder is the best for obtaining those water molecules being within x nm of protein? -- 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_Lis

[gmx-users] g_select vs trjorder

Dear Tsjerk and Mark Thanks for your time and attention. using g_select -f *.xtc -s *.tpr -n index.ndx -oi -select '"Close to Protein" resname SOL and within 0.25 of group Protein' solved my problem. I want to use trjorder -f *.xtc -s *.tpr -n index.ndx -o ordered.pdb -nshell -r 0.25 -na 3 -da 1

[gmx-users] g_select problem (Invalid command line argument:)

Dear Justin Thanks for your reply. As you said " You need to enclose your selection string within ' ' so it is interpreted as a single string." , I enclosed my selection string: g_select -f com_ta_full_3.xtc -s com_ta_full.tpr -n index.ndx -oi -select "Close to Protein" 'resname' 'SOL' and with

[gmx-users] g_select problem (Invalid command line argument:)

Dear gromacs users My system contains protein and water molecules. I want to use g_select to obtain residue number of water molecules being within 0.35 nm of protein. My index file is as follows: [ Protein ] [SOL] When I use g_select -f *.xtc -s *.tpr -n index.ndx -oi -select "Close to Prot

[gmx-users] adding base pairs to dna pdb file

Dear gromacs users I have a pdb file (10 base pair) containing a specific damage being my favourite for md simulation study. The damaged nucleic acid is in the last but one. I want to add at least 5 base pair to original pdb file. How to do that? What program can help me? Any help will highl

[gmx-users] g_analyze -ee

Dear all I used g_analyze -f dist.xvg -ee In the one of the my output files, I encountered Read 1 sets of 1252 points, dt = 0.0119951 std. dev.relative deviation of standard - cumulants from those of set

[gmx-users] g_analyze -ee

Dear gromacs users I want to calculate error estimates using block averaging for output from g-dist (distance between donor atom of protein and acceptor atom of dna). I used g_analyze -f dist.xvg -ee there are 3 columns in output file. anyone give me more explain about these columns? how to e

[gmx-users] how to obtain error bar for plotting?

Dear Mark can I obtain error bar twice the standard error of the average distance between the donor atom of protein and acceptor atom of dna over 1 simulation? should I do several simulation. Is 1 simulation enough? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mai

[gmx-users] how to obtain error bar for plotting?

Dear Mark I am studying interaction between protein and dna, especially hydrogen bonds. using g-dist, I obtained distance between donor atom of protein and acceptor atom of dna. in this case, can I use g_analyze for obtaining error bar or stddev? -- gmx-users mailing listgmx-users@gromacs.o

[gmx-users] how to obtain error bar for plotting?

Dear Mark thanks for your reply. I have a general questions: For what parameters I can use g_analyze -av average.xvg -errbar stddev -f *.xvg?* What quantity do you wish to show with an error bar? I want to show output from g_dist with an error bar. -- gmx-users mailing listgmx-users

[gmx-users] how to obtain error bar for plotting?

Dear all For what parameters I can use g_analyze -av average.xvg -errbar stddev -f *.xvg? Can I use above tool for obtaining error bars for a *.xvg file resulting from g_dist? I want to obtain a file (containing error bar) to plot with excel. Best Regard -- gmx-users mailing listgmx-users

[gmx-users] how to obtain error bar for plotting?

Dear Mark Thanks for your quick reply. For what parameters I can use g_analyze -av average.xvg -errbar stddev -f *.xvg? Can I use above tool for obtaining error bars for a *.xvg file resulting from g_dist? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/list

[gmx-users] how to obtain error bar for plotting?

Dear gromacs users In the average file, there are 3 columns: first column is time, second is rmsd value. third column is 0. what is third column? best regards. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] how to obtain error bar for plotting?

Dear gromacs users I would like to calculate the standard deviation (as the error bar) for rmsd.xvg file. If rmsd.xvg was used in excel software, it gives a graph as rmsd vs time. I want to have a file containing rmsd vs time and error bar relating to rmsd values such that after plotting by exce

[gmx-users] trjconv -pbc mol/nojump

Hi, You should use trjconv in 2 steps: (1) trjconv_d -s md_100ns.tpr -f md_100ns.xtc -o md_100ns_pbc_nojump.xtc -pbc nojump in this step, select system for output (2) trjconv_d -s md_100ns.tpr -f md_100ns_pbc_nojump.xtc -o md_100ns_pbc_mol_center.xtc -pbc mol -center in this step, select sol

[gmx-users] How to obtain and how to use acpype

Dear Kavya Thanks for your attention Unfortunately, I don't access to http://code.google.com/p/acpype/ Your client does not have permission to get URL /p/acpype/ from this server. Please guide me. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

[gmx-users] How to obtain and how to use acpype

Dear gromacs users I want to do MD simulation of protein-ligand. I read a tutorial by John E. Kerrigan "Tutorial for Trypsin-Benzamidine complex molecular dynamics study." in which they used acpype. I want to know what is acpype? a program in gromacs or amber or a pythone file? please explain ab

[gmx-users] xvg plotting

Hi Nicole In linux/unix, there are a program named xmgr aor xmgrace by default. Just you type in command line : xmgr 1.xvg 2.xvg 3.xvg .. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing

[gmx-users] g_confrms and superimposed structures

Dear Justin Thanks for your attention My problem was solved. I have a new question. as I said my goal is superposition of averaged md structure and x-ray structure. My simulation is 5 ns. How to obtain the MD structure average for the period 1.5–5 ns? what command? -- Leila Karami Ph.D

[gmx-users] g_confrms and superimposed structures

tures simultaneously in one figure? (my goal is superposition of averaged md structure and x-ray structure) -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] g_confrms and superimposed structures

Dear gromacs users I know There are two models. VMD loads them as sequential frames such that they can be animated (frame "0" and "1"). I want to have 2 structures simultaneously and not as sequential animation. -- Leila Karami Ph.D. student of Physical Chemistry K.N.

[gmx-users] g_confrms and superimposed structures

? any help will highly appreciated. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] how to cite gromacs?

Dear gromacs users I want to know how to cite gromacs version 4.0.7? what paper do relate to that? -- 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 postin

[gmx-users] water-medited hydrogen bonds - %exist hydrogen bonds

, please guide me about that. any suggestion will highly appreciated. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] %exist hydrogen bond - difference between number of lines in input and output files

0.080 please explain this differences more. best regards. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] %exist hydrogen bond

11.191 SOL1805OW LEU26 O0.160 SOL1805OW SER27 N0.160 best regards -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group

[gmx-users] %exist hydrogen bond

Dear Justin yes, I deleted my previous "summary_HBmap.dat" before running the modified script. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromac

[gmx-users] %exist hydrogen bond

61.711 ASN51 OD116.867 ASN51 ND2 0.320 GLN23 OE111.191 . . . how to fix it? -- Leila Karami Ph.D. student of Physical Chem

[gmx-users] %exist hydrogen bond

1.839 ARG58 NH1 0.080 ARG58 NH1 21.663 What is problem? Please guide me about that. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of

[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file

atoms. is it true? why did you use r,a,b,c=range,1868,24086,24100. is r,a,b,c=range,1867,24085,24099 wrong? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromac

[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file

for example ordering in final.pdb is as follows: ATOM 1856 N2 DG3 X 86 15.620 47.770 21.660 1.00 0.00 ATOM 1857 H21 DG3 X 86 16.480 48.290 21.560 1.00 0.00 ATOM 1858 H22 DG3 X 86 15.010 48.060 22.420 1.00 0.00 ATOM 1859 N3 DG3 X 86 14.160 46.250 20.

[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file

Dear Justin and Chris very thanks for your reply and guidance. I did all the steps successfully. then I used (./my_tool -f final.xtc -o final.pdb -b 300 -e 350), the final.pdb file was created without problem. when I opened final.pdb file by text editor, order of waters and ions in final.pdb was

[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file

Dear Chris very thanks for your time and attention. only difference between what you said and what I did is in the location of template directory: for me gromacs-4.0.7/share/template for you gromacs-4.0.7/exec/share/gromacs/template in my gromacs there is not exec dire

[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc message

Dear Chris I did all of steps again. this tims when compile Makefile.my_tool by both of make and gmake: make: *** No rule to make target `my_tool.o', needed by `my_tool'. Stop. my Makefile.my_tool is as follows: # Generated automatically from Makefile.in by configure. # # This is a Gromacs 3.0

[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file

Dear Chris I found gmx_trjconv.c file, It is in gromacs-4.0.7/src/tools. since location of template directory is as follows: gromacs-4.0.7/share/template, I used cp gmx_trjconv.c ../../share/template/my_tool.c. is it true? I did those changes you said in my_tool.c file. I created makefile without

[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file

Dear Chris Happy new year thanks for your reply. please clarify these more: cd src/tools cp gmx_trjconv.c ../../exec/share/gromacs/template/my_tool.c 1) where is exact location of gmx_trjconv.c file? when I enter cd /src, in src directory, there is not tools directory. 2) in my linux, gromacs

[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file

suggestion will highly appreciated. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Segmentation fault in g_hbond

Dear Erik there are several hb->per->pHist in gmx_hbond.c. please say me exactly in which part of the gmx_hbond.c file if-statement should be placed? If I install gromacs 4.5.2 or 4.5.3, is there not this problem (segmentation fault)? -- Leila Karami Ph.D. student of Physical Chemist

[gmx-users] Segmentation fault in g_hbond

Dear Erik excuse me, I sent .xtc and .tpr file your e-mail. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Segmentation fault in g_hbond

bugzilla and attach a tpr and xtc/trr? I don't know. size of xtc file is large, how to attach this file to list? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Segmentation fault in g_hbond

Dear Erik I used g_hbond in 4.5.1 but problem was not solved. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Segmentation fault in g_hbond

Dear gromacs users I'm using gromacs 4.0.5. with following command: g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn. my system contains protein, dna and water. when I use above command for protein and dna, there is no problem. segmentation fault is only for protein and water. -- Leila K

[gmx-users] Segmentation fault in g_hbond

Dear gromacs users I used g_hbond tool for hydrogen bond analysis between protein and solvent (water molecules). I have encountered with : Select a group: 3 Selected 3: 'Protein' Select a group: 15 Selected 15: 'SOL' Checking for overlap in atoms between Protein and SOL Calculating hydrogen bon

[gmx-users] conversion of gromacs files to amber files

pt to change the pdb file for compatibility with amber. please share me that. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinf

[gmx-users] conversion of gromacs files to amber files

Dear Oliver Grant thanks for your attention. I want to use amber tool for hydrogen bond analysis especially (water mediated hydrogen bonds and residence time and occupation of them). -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical

[gmx-users] conversion of gromacs files to amber files

Dear gromacs users I did simulation of protein-dna by gromacs and amber03 force field. I want to do some analysis by amber. what is the best way for conversion of gromacs trajectory and topology files to amber files? any help will highly appreciated. -- Leila Karami Ph.D. student of Physical

[gmx-users] g_select / Input error or input inconsistency

- Program g_select, VERSION 4.5.1 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Document

[gmx-users] g_select / Input error or input inconsistency

Dear Justin I made new .ndx file in which there are following groups: protein protein-H DNA DNA-H SOL I changed selection.dat file to waterO = group SOL and name OW; heavy1 = group Protein-H; heavy2 = group DNA-H; inter = waterO and within 0.3 of heavy1 and within 0.3 of heavy2; inter; but aga

[gmx-users] g_select / Input error or input inconsistency

protein and DNA* *and not protein or dna.* * * * -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

[gmx-users] g_select / Input error or input inconsistency

rors Am I doing it incorrect ? Is there problem in my .ndx file? Is this error a bug in gromacs 4.5.1? Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gro

[gmx-users] perl script for g_hbond

ctory. and also you said I need to create a corresponding index file too. I don't know where should I start for multiply two existence functions? please explain about it more. any help will highly appreciated. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of

[gmx-users] perl script for g_hbond / summary_HBmap.dat

g the existence functions how to multiply these two existence functions? how to make new index file? should I write those lines from two hbond.ndx file above in which particular water hbonds to both protein and DNA? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi Universi

[gmx-users] perl script for g_hbond / summary_HBmap.dat

Dear Erik I'm confused. is there h(t) in hbmap.xpm file? where is h(t)? which output file of g_hbond tool? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] perl script for g_hbond / summary_HBmap.dat

lp me? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Su

[gmx-users] perl script for g_hbond / summary_HBmap.dat

obtaining of hbond.ndx and hbmap.xpm files from g_hbond tool, what groups should be select? in previous state (protein-dna direct hydrogen bond), I selected 1) protein and 2) dna. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical

[gmx-users] perl script for g_hbond / summary_HBmap.dat

. 3) I think that %exist should be determined for each of donor-hydrogen-acceptor being in hbond.ndx file.Isn't it? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] perl script for g_hbond

in('', $resn, $resnum); } } } } } # open a single output file for writing open(OUT, ">>summary_HBmap.dat") || die "Cannot open output file!\n"; printf(OUT "%10s\t%10s\t%10s\t%10s\%10s\n", "#Donor", "

[gmx-users] perl script for g_hbond

Dear Justin when I use perl HB.pl -s .pdb -map .xpm -index .ndx, I encountered with: syntax error at ./HB.pl line 10, near "nothing else" "use" not allowed in expression at ./HB.pl line 13, at end of line Execution of ./HB.pl aborted due to compilation errors. -- Leila

[gmx-users] perl script for g_hbond

Dear Justin thanks for your time and attention yes of cource, I copy and paste correctly entire script from (first line) # ! /usr/bin/perl to (last line) exit. what is your mean of [There should be more information in the output if the program fails]? which output? -- gmx-users mailing listg

[gmx-users] perl script for g_hbond

Dear Carla thanks for your attention I used : perl HB.pl -s .pdb -map .xpm -index .ndx, but problem is there yet. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] perl script for g_hbond

Dear Justin I study simulation of pr-dna complex. I want to know the percentage of existence of each hbond during my trajectory. I searched in previous lists. I want to use Perl script you offered to carla jamous: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054727.html I'm biginner

[gmx-users] water molecules (interfacial)

Dear gromacs users I was trying to count waters involved in the interface between Protein_A and Protein_B. I made a selection.dat file as follows: waterO = group SOL and name OW; heavy1 = group Protein_A and group "Protein-H"; heavy2 = group Protein_B and group "Protein-H"; inter = waterO and wi

[gmx-users] water molecules (interfacial) - IIRC

Dear Mark I have a question as same as atila petrosian, but my system is protein-dna. you said [IIRC g_select has some better documentation available once you run it and ask for help, somewhat like make_ndx]. please explain IIRC more. Is IIRC a program or a list of archives? any help will highl

[gmx-users] kind of contacts in protein-dna interaction during simulation

Dear Mark thanks for your attention. I read manual before. I know that g_hbond is for hydrogen bond analysis. But I don’t know about Van der Waals interactions analysis and how to obtain percentage of them. Please give me more information about what I said. -- Leila Karami Ph.D. student of

[gmx-users] kind of contacts in protein-dna interaction during simulation

integrase protein: a molecular dynamics analysis. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] center peptide in simulation box

- one to center the peptide and one to group the waters in the same periodic cell as the peptide. I want to know how can I do last (group the waters in the same periodic cell as the peptide)? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical

[gmx-users] Fwd: -pbc nojump

Dear Tsjerk Thus, as you said, Xtc file obtained from trjconv –pbc nojump only concerns visualization. Thus, can I use old xtc file (with out –pbc nojump) for analysis such as interfacial waters and water mediated hydrogen bonds or every other analysis? -- gmx-users mailing listgmx-users@gro

[gmx-users] Fwd: -pbc nojump

Dear Carsten and David and Tsjerk Thanks for your time and attention My purpose of these questions is to find a way that 1) close two separated strand of dna (in my case only –pbc nojump fix it) and also 2) water molecules to be put in interface of between protein and dna. Because I want to sur

[gmx-users] Fwd: -pbc nojump

Dear Tsjerk I did what you said: 1. trjconv -f a.xtc -s a.tpr -o 1.xtc -pbc nojump (system for output) 2. trjconv -f a.xtc -s a.tpr -o 2.xtc -pbc mol –center (pr/dna for centering, system for output) Now, I need new trajectory file for analysis. How I obtain new trajectory file fr

[gmx-users] Fwd: -pbc nojump

Hi Carsten Thanks for your answer. You got my case very well. I understand your mean as follows: 1) Trjconv –f a.xtc –s a.tpr –o b.xtc –pbc mol (output group=water) 2) Trjconv –f a.xtc –s a.tpr –o c.xtc –pbc nojump (output group =protein-dna) Is that true? You said, (Then over

[gmx-users] interfacial water molecules

Hi gromacs users Since I study dynamic of interfacial water molecules between protein and dna, I want to know, is there any keyword in gromacs to obtain number of interfacial water molecules between protein and dna as a function of simulation time? Is there any way which water molecules put in int

[gmx-users] -pbc nojump

Dear Mark my mean of [when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group.] is that the problem (nonentity of water molecules in interface of protein and dna) was not solved. what is your mean of [You might need two passes with

[gmx-users] -pbc nojump

Dear Mark thanks for your attention when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http:

[gmx-users] -pbc nojump

Hi gromacs users I study simulation of protein-dna interaction using gromacs. After full md simulation, because of diffusion of one strand of dna to edge of box, I used trjconv -f old.xtc –o new.xtc –s *.tpr -pbc nojump -ur compact –center. By this way my first problem is solved. 1) Should I

[gmx-users] simulation of a protein including calcium ion

Dear Justin Is there any way for this problem? -- 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 l

[gmx-users] simulation of a protein including calcium ion

Dear Justin thanks for your attention in my case calcium ion is bonded to 4 oxygen atoms of C=O group of protein. yes, Calcium ions are present in nearly all the force fields in Gromacs. but there are only parameters in * nb.itp and not in * bon.itp. how to obtain these new parameters for my case

[gmx-users] simulation of a protein including calcium ion

Dear mohsen ramezanpour my pdb file has 3000atoms (protein) + 1 atom (calcium). Should I separate ion from general pdb again? -- 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/Maili

[gmx-users] simulation of a protein including calcium ion

Dear mohsen ramezanpour* * yes. calcium is a typical ligand in my pdb file.I used PRODRG server to make topology file but ERRDRG> Too many atoms in this molecule (should be <=300). PRODRG> Program terminated unsuccessfully, sorry! -- gmx-users mailing listgmx-users@gromacs.org http://lists.g

[gmx-users] simulation of a protein including calcium ion

Hi gromacs users I want to study simulation of a protein including calcium ion. Can I use gromacs force fields? any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromac

[gmx-users] deletion of some water molecules

Dear Erik Marklund thabks for your attention I want only have water molecules being in 1.5 nm of solute in final frame (2 ps) I used following command: trjorder -f *.xtc -s *.tpr -n *.ndx -o *.gro -r 1.5 -b 2 is it true? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gr

[gmx-users] deletion of some water molecules

Dear gromacs users I did simulation of protein-dna complex in a box with size 7,7,7. There are 5000 water molecule in this box. After full md simulation, I need a pdb or gro file containing only water molecules being exactly environment of pr-dna complex and not water molecules being in edges or

[gmx-users] wrong string length 0 for string buf

Hi gromacs users When I uesed command : trjconv -f com_full.xtc -s com_full.tpr -n com.ndx -o com.xtc -pbc nojump -ur compact -center gromacs gives me the following error: Program trjconv, VERSION 4.0.5 Source code file: gmxfio.c, line: 609 Fatal error: wrong string length 0 for string buf (so

[gmx-users] pdb file

Hi gromacs users I obtained pdb input file for gromacs from STRAP program. this pdb file coantains protein and dna. this pdb file was obtaind form superposition of 2 other pdb files. there is one problem: when I see pdb file obtained from STRAP program by VMD, some bonds are disappeared whereas wh

[gmx-users] visual program

Hi gromacs users is there visual program other than VMD for seeing trajectory obtained from gromacs? thanks in advance. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting

[gmx-users] b-factor

Hi all pdb file for my protein was obtained by solution NMR. this file is as follows : ATOM 1 N GLY A 1 -25.349 -8.577 4.055 1.00 0.00 ATOM 2 CA GLY A 1 -24.037 -8.099 4.448 1.00 0.00 ATOM 3 C GLY A 1 -23.580 -6.913 3.622 1.00 0.00 ATOM

[gmx-users] g_msd and diffusion coefficent

Dear Vitaly Chaban yes. my md simulation is equilibrioum. I did simulation of protein-dna. I want to know how protein and dna close together and interact together (approach of protein to major groove of dna). thanks alot in advance. -- gmx-users mailing listgmx-users@gromacs.org http://list

[gmx-users] -dt

Hi gromacs users I want to know what is purpose of -dt flag in most of commands? in my analysis, different values for -dt results in outcomes have not determined trend . I used this flag for g_rms as follows : if g_rms -f pr.xtc -s pr.tpr -n pr.ndx-o 5.xvg -dt 5 so : gromacs record out

[gmx-users] b-factor

Hi all pdb file for my protein was obtained by solution NMR. this file is as follows : ATOM 1 N GLY A 1 -25.349 -8.577 4.055 1.00 0.00 ATOM 2 CA GLY A 1 -24.037 -8.099 4.448 1.00 0.00 ATOM 3 C GLY A 1 -23.580 -6.913 3.622 1.00 0.00 ATOM

[gmx-users] g_msd and diffusion coefficent

Dear Vitaly Chaban I know using index file but gromacs say : select only 1 group. what is this group ? protein? or DNA? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting!

[gmx-users] g_msd and diffusion coefficent

Dear Mark Abraham No, I want to measure something about the diffusion of my protein to DNA (especially to major groove of DNA) in the presence of water (as solvent). -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive a

[gmx-users] g_msd and diffusion coefficent

Dear Mark Abraham yes. pr means protein. I want to obtain diffusion of protein within dna. I want to know how/how much pr diffuse to dna. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/sea

[gmx-users] g_msd and diffusion coefficent

Hi gromacs users in my system, there are pr, dna, water and Na and I want to obtain diffusion of pr in dna but when I use g_msd command, gromacs says select only 1 group. should be this group pr or dna? Thanks a lot in advance. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gro

[gmx-users] g_msd and diffusion coefficent

Hi gromacs users I did simulation of pr-dna by gromacs. I want to obtain diffusion coefficent of pr to dna. I raed manual (g_msd) in which there are diffusion coefficent only for 1 and 2 dimension as follows respectively : -type : Compute diffusion coefficient in one direction: no, x, y or z -l

[gmx-users] cgnr in top file

Dear Erik you said Amber03 was not parameterized with charge groups and last column in your rtp entry holds the chargegroup numbers. but cgnr column in my top file does not looks just like it. in case of H1, H2 and H3. * H1amber99_17 0.16420 2 ** H2amber99_17 0.16420 3

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