[gmx-users] Gravity or weightlessness condition

Dear I want to simulate cell membranes in weightlessness condition ( the same as space).Would you please tell me Can I run with Gromacs? If Yes with which parameters? Best -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the arc

[gmx-users] g_covar

Dear Justin Hi,I want to use PCA for compare fluctuations two peptides with 13 aa. I use this command g_covar g_covar #NAME? run2.tpr#NAME? run2.xtc#NAME? eigenvaluesbackbone.xvg #NAME? eigenvectorsbackbone.trr#NAME? covarbackbon.xpm and get the some of data : ti

[gmx-users] g_covar

Thank you justin and his colleagues and you Mr Tsjerk. -- sh-karbalaee -- 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)

[gmx-users] error in creat topology

Dear justin I want to creat topology file tfe by ffopls.I get pdb file tfe and add atoms and bond tfe atoms to ffoplsrtp file in top file gromacs.so in hdd I add hydrogen atoms.when I do pdb2gmx -f tfe.pdb.I get this message: Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp

[gmx-users] NH2 IN CTERMINAL

Dear justin Hi, In my simulation with ff53a5 when I do this command pdb2gmx -f name.pdb -ter -ignh -water spce .I find this error .C-terminus: None Now there are 14 residues with 138 atoms Making bonds... Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Number of bonds w

[gmx-users] error NH2 in C terminal

Dear Justin Thank you for your advice. there is NH2 in c terminal sequence peptide but when I do pdb2gmx I get error.I delete NH2 by hand and do pdb2gmx -f name.pdb -ter and choose none in c terminal .when I see top file I see NH2 add in C terminal.Is it correct? and another way I use missin

[gmx-users] steady

hi justin in during making mix solvent (30% for example) after making box I use trjconv -pbc .My pdb file lost the the arrange and it need long time for equilbrate and steady density.Is it right? or any suggestion about it? thanks -- sh-karbalaee _

[gmx-users] steady

Dear justin you are right .that file was distorted.I used -pbc without no jump.I need to use trjconv for minimized the box .please advise me. -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gm

[gmx-users] steady

Dear justin I made a file with (n1/n2=30) two solvents.I want to equilbrate this file.then I must minimize and run md(pre md ).please correct me if It is not right. I use editconf -f test42.pdb(this file)-bt dodecahedron - d 0.5 -o box.gro as you tell for delet periodicity editconf -f

[gmx-users] steady

excuse me for bad typing in english. how can I understand the solvents file equilbrated?from rmsd or visualization or ..? -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] steady

thank you justin . would you please tell me how can it equilbrated?is it the table rmsd aor visualization?or the time pr-md for 10 ns is enough (for tfe and spce)? -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs

[gmx-users] steady

Dear justin a) if I want to have the steady and hemogen for mix solvent , do I have to use this command (when I made genbox box 16.16.24 before that)? :editconf -f conf.gro -bt dodecahedron -d 0.5 -o box.gro b) I use trjconv -pbc mol -ur compact and then minimize .when I see the output this

[gmx-users] tcoupling

hi justin I have a file tfe peptide water,cl .I minimized it and I want to preequilbrate it.when I do the grompp I get 1 warning: calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 turning all

[gmx-users] tcoupling error

Dear thanks for your answer. I did as you tell me about usingcapital letter .about charge I guess it related to tfe and protonated amino acid.after change it I still have this warning. best -- sh-karbalaee ___ gmx-users mailing listg

[gmx-users] tcoupling

Dear justin ok.you areright.if I add another cl- ,it will negative than more.I know my peptide of charge is +1.please tell me no problem if with warning continue. --best sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs

[gmx-users] dielectric coffiecient

Deat justin thanks for your help. I delete cl- from (peptide,tfe ,water) in my system and I see about his charge not get message. when I add tfe in peptide (pdb2gmx -f name.pdb -ter -ignh )the lysin amino acid is protonated (2 lysin).another charge aminoacid is D,E.do you think it related to adding

[gmx-users] n terminal

thank you justin in papers net charge of peptide is calculated +1,with amidated in terminal. that I defined with flag -ter in pdbf2gmx .and when I add tfein system I see in pdb files lys is changed LYSH. best -- sh-karbalaee ___

[gmx-users] versiongromacs

Dear justin hi, I minimized my peptides with gromacs 3,3,3 .Can I use this files (em.gro) for pr and md with gromacs 3,3,1.? best -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-user

[gmx-users] version gromacs

Dear justin thank you.No ,because nothing enough free spce I must do MD on another pc with version 3,3,1.but I donot get problem and my result is good.what is your idea?Is it right.? -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.or

[gmx-users] position restrain

Dear justin can I use pcouple=yes in pr.mdp ?what is defferent in my data when I use pcouple=no? best sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive a

[gmx-users] time of dynamic

Dear Justin/mark would you please tell me for compare dynamic peptide what time for MD is enough by gromacs?generally. I think 20ns enough ,what do you think? many people suggest 120ns best -- sh-karbalaee ___ gmx-users mailing listgmx-users@g

[gmx-users] error

hi Dear justin would you please tell me about this error.I run by gromacs version 3.3 and my file consist of peptide,tfe ,water.I want to minimize that I get this error. Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps= 2000 -

[gmx-users] g_rmsd

Dear justin I want to calculate rmsd or rmsf from avg structure.Infact I calculate standard deviation from average structure.Can I do it with command g_rmsf and g_rmsd?thanks for your advise. best sh-karbalaee ___ gmx-users mailing listgmx-users@gro

[gmx-users] jump peptide

Dear Justin/Mark hi I have a system with peptide and tfe/spc .I minimized and run for equilbrate them for 5 ns.when the pr-md was end the time.I saw the gromac file by vmd.the peptide jump from the box .but when I saw ngmx and choose triclinic ,the peptide was insert in box.I have chosen - bt do

[gmx-users] pbc

Dear justin thank you.I read pbc subject.and I know that it solve trjconv .now if I use trjconv after premd . is it still right.? best -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-use

[gmx-users] pbc

Dear justin ok thank you . I really thanks for your answer. best -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before po

[gmx-users] capping in c terminal

Dear justin Hi, about NH2 in c terminal peptide,do we need to chang rtp file for last aminoacid,although there is NH2 in that and define it?or is it enought to have pdb file and choose none option for c termial? best and hope you are ok. sh-karbalaee

[gmx-users] rmsd

Dear justin I have rmsd graph from peptide (13 amino acid).would you please tell me about generally range of rmsd for good simulation.In my table rmsd start from 2 nm and come up to 3 and change between 3 to 3.5 nm.the solvent is tfe/water.thanks for your advise. best regards -- sh-karbalaee

[gmx-users] visualize atom number backbone

Dear justin I want compare two rmsf atoms from two peptide(backbone).then I need have atom in backbone. there is the column lable atoms .but in spdbv ,atom numbering for backbone is simillar peptide (backbone+side chain).would you please tell me for visuallize atom numbering backbon ,what do I do?

[gmx-users] define atoms

Dear mark excuse me. I attempt it again.in analysis result of md peptide I have the table t consist of atoms number column and the other column rmsd(nm).I want to know what is thename of atom which define number 12 in backbone group ?Is it NCC for example related to ser or another aminoacid

[gmx-users] define atoms

Dear justin how do I know,what is the name ofatom 17 in rmsf table of backbone group.? # g_rmsf -f md.xtc -s md.tpr -o traj_rmsfbackbon.xvg -ox traj_avgazrmsfbackbon.pdb # # g_rmsf is part of G R O M A C S: # # God Rules Over Mankind, Animals, Cosmos and Such # @title "RMS fluctuation" @

[gmx-users] a question

dear sir/madam I am doing MD ap peptide with gromacs.this peptide( 13 residue) has a NH2 in c terminal.I change it from heteroatom to atom but it take a error.and it say :I acnnot find C alpha for residue 14 NH2 WHILE COMBINING tdb and rtp.what do i do ? best -- sh-karbalaee __

[gmx-users] rtp file

hi my peptide(13 aa), has a NH2 bond in C terminal.I must rtp file for modified amino acid (phe -NH2). and another else that I dont know.please say to me what do i do if i want run md with this peptide.? Do I need to change hdb file and amino acid .dat?.please help me. -- sh-karbalaee

[gmx-users] rtp files

hi again please send me rtp file for phenylalanin- amide. thanks -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before po

[gmx-users] question

Dear I donot get your answer.I have a peptide with NH2 bond in C terminal.Can I run MD with gromacs generally ?.or It shall know that as modified residue. when I run it I have this error: I donot find c for 14 residue.(it is NH2 in c terminal). -- sh-karbalaee ___

[gmx-users] question

Dear mark. that is right.NH2 were heteroatoms.and the gromacs take error for it because "the residue 14 (=NH2) donot have ca.then I changed it in pdb file to atom.but it doesnot accept. NH2 in c terminal make sense coo- and one bond NH2.Do i delete heteroatom and run md it? thanks -- sh-karbala

[gmx-users] Re: gmx-users Digest, Vol 48, Issue 95

:23 +0300 (EEST) > From: Satyan Sharma <[EMAIL PROTECTED]> > Subject: [gmx-users] question > To: gmx-users@gromacs.org > Message-ID: <[EMAIL PROTECTED]> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > shahrbanoo karbalaee wrote: > > > > Dear > > > &

[gmx-users] get structures

Dear all and Mark hi, I want to get structures peptide during MD.(format pdb).how can I get it? and the scond question, Dear Mark,IF I want to have average structure what do i do?let me explain it. the peptide during MD has many structure.which structue is insert in middle structures? and th

[gmx-users] g_dist

Dear Mark I want to calculate distance ca_ca from the third residue to the ninth residue during MD .but i dont know identify in command number of residue. g_dist -f name.xtc -s topol.tpr -b 0 -e 20 -dt 0.002 and the second, can i get average distance by a command. thanks for your advice --

[gmx-users] genion

Dear justin thanks for reply about g_dist. about genion for peptides.Do I must use command genion for MD peptides with one charge(13 aa)?Is it necessary for md? best sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

[gmx-users] Is it correct

Dear justin In my work MD peptide(with 13 aa) I use this md.mdp.would ypu please say me Is that correct. title = cpeptide MD cpp = /lib/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 5000

[gmx-users] Re: gmx-users Digest, Vol 51, Issue 85

___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface

[gmx-users] Re: gmx-users Digest, Vol 51, Issue 85

> -- > > Message: 3 > Date: Wed, 23 Jul 2008 18:14:50 +0430 > From: "shahrbanoo karbalaee" <[EMAIL PROTECTED]> > Subject: [gmx-users] Is it correct > To: gmx-users@gromacs.org > Message-ID: ><[EMAIL PROTECTED]> > Content-Type: te

[gmx-users] Re: gmx-users Digest, Vol 51, Issue 89

Dear justin Thank you again. but about if i use TFE for solvent instead of water ,how can apply dielectric constant in program and only I can TFE instead of spc/e.what about PH?and counter ion ? best karbalaee ___ gmx-users mailing listgmx-users@grom

[gmx-users] tfe

Dear mark and justin hi,thank you for your advices. I want to make simulation peptide in 30%tfe.I get tfe.pdb and take tfe.gro from prodrug program.I make solvatedtfe.gro and the other solvatedspc.gro.then I make 30mol tfe and 70 spc in a file by hands.and then run genbox -f .cs 3tfe70spc.gro .

[gmx-users] tfe

Dear justin and mark hi again I work in tfe.pdb with polar hydrogen from prodrg.and with commnad genbox -cp -- ci tfe.gro -nmol 50 -o mtfe.gro ANDcommand genbox -cp mtfe.gro -cs -out2 make the file peptide ,tfe ,water .then by change number the mole it will make 30%.and edit topology fil

[gmx-users] tfe

Dear justin I try again .but I get this error toputil .line 1364 not found such molecoule SOL.then would you please check my topol.top file and advise me. PEPTIDE A5 OR AUREIN 1.2 ; ; Include forcefield parameters #include "ffoplsaa.itp" [ moleculetype ] ; Namenrexcl Protein_A

[gmx-users] tfe

Dear justin I trap in local minma.I dont know. Now after edit topolgy file I get error again.not found C type.I make tfe.pdb and tfe.gro in prodrg and try it again editconf for change pdb to gro file. I saw source code toputil line 61.not found C type. best-- sh-karbalaee __

[gmx-users] tfe

Dear justin here it is. creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6# WARNING 1 [file em.mdp, line unknown]: Unknown left-hand 'constrains' in parameter file WARNING 2 [file em.mdp, line unknown]: Unknown left-hand 'nslist' in parameter file check

[gmx-users] tfe

Dear justin as your telling I have two way for my problem: 1-choose force field that is compatible to TFE(with 7 atom) that I used another force field.I made tfe.pdb (with 7 atom) and choose gromos 96 but I got error that dont found HO atom. 2)another way,I must itp file for tfe with opls forcefiel

[gmx-users] tfe.itp

Dear justin I made topology top for tfe with gromos53a5.and I solvated in spc and 40molecule tfe.I includeed tfe.itp in topology.but when I do grompp I get this error.(I edit the name of atoms with name in rtp file HT) Generated 165 of the 1596 non-bonded parameter combinations ERROR 0 [file "topo

[gmx-users] tfe.itp

Dear justin after edit tfe.itp , I did the command grompp and I got this error : error input solvated.gro. Do I have to make spc.gro with tis forcefield(gromos965a)? best -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http:/

[gmx-users] tfe

Dear justin for have tfe30% after I got tfedrg.top with pdb2gmx and force field gromos965a. I do t this command : editconf -f tfedrg.gro -bt dodecahedron -d 0.71 -o box.gro genbox -cp box.gro -cs spc216.gro ci tfedrg.gro - nmol 40 -p topol.top -o solvated.gro I did that command with spc.gro(I

[gmx-users] tfe and gromos9653a

Dear justin I guess I did right.I add in my topoly file tfe in part of dehedrals " gd_24".(from your edit in dmso topolgy last another mail)and I could minimize. what do you think this adding ?.any way thank you for every thing.now about my peptide I have this error .(in c terminal peptide i

[gmx-users] ffg53a5

Dear justin I cannot find my error.I make mix solvent tfe and spc ( was minimized)and solvate on a peptide.I use ffg53a5 .I take this error .I saw in line 61 in top file but there is not Ho in top file and rtp file ffg53a5. what do i de?please help me. Back Off! I just backed up mdout.mdp to .

[gmx-users] error ffg53a5

Dear justin here it is .the files is attached.I insert gd-29 in line before the last line (dehidral) so . best -- sh-karbalaee ; ; File 'topol.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Thu Aug 21 23:30:46 2008 ; ; This is your topology

[gmx-users] error ffg53a

Dear justin as you wrote, the first I make tfe.topology with this force field by command pdb2gmx and pdbfile from prodrg.and add to box with spc.now I have the file spc and tfe.by command grommp I minimized this file .I got a file emsolve.after this ,I work on this peptide . pdb2gmx -f name -

[gmx-users] error ffg53a and thanks

Dear justin mer30.and thanks .you are great.I do it as you tell me.and work. best wishes sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.or

[gmx-users] error in solvation

Dear justin I hope u r ok.I make tfe 30%in water with genconf and genbox.after that I minmized and equilbrated this mix solvent for 14ps.and with command trjconv got the last pdb file.this file (last pdb file)was solvated.gro(editconf).now I want to insert peptide in solvated.gro but donot insert