Re: [gmx-users] HC atomtype
when I'm trying to use the Tielman's lipid.itp I always have the following error message: Second default directive found in lipid.itp line ... [defaults] in lipid.itp are defined after [defaults] in ffgmx.itp because ffgmx.itp shuld be included before lipid.itp. I wonder if I can just delete [defaults] from lipid.itp. How to fix this problem? thanks > > or if i put ";" in the line 9 of lipid.itp atomtype LC3 not found > > or if i put ";" in the line 9 of lipid.itp and put > > [ defaults ] > > ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ > > 1 1 no 1.0 1.0 > > > > in the .top file, the same error comes. > > --- Mark Abraham <[EMAIL PROTECTED]> wrote: > > Dear all > > I want to run grompp command for making .tpr file > of > > POPC+Protein.I've been using the > ffgmx.itp,lipid.itp > > and i've removed the lipid.itp of the > > .top file, but it gives a fatal error : > > Atomtype 'HC' not found! > > Any help will be highly appreciated. > > I'm guessing HC will be defined in lipid.itp. Why > take it out? > > Mark > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > Yahoo! oneSearch: Finally, mobile search that gives answers, not web links. http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] HC atomtype
Dear all I want to run grompp command for making .tpr file of POPC+Protein.I've been using the ffgmx.itp,lipid.itp and i've removed the lipid.itp of the .top file, but it gives a fatal error : Atomtype 'HC' not found! Any help will be highly appreciated. thanks Tonight's top picks. What will you watch tonight? Preview the hottest shows on Yahoo! TV. http://tv.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] itp files
Dear all I want to simulate protein in popc.i inserted protein in popc(vmd). which itp files are suitable for this simulation(protein,popc)?how can i make top file by pdb2gmx or not? thanks Pinpoint customers who are looking for what you sell. http://searchmarketing.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] protein in membrane
Dear all i want to insert protein in popc.which practical protocol in gromacs is useful for me? thanks Tonight's top picks. What will you watch tonight? Preview the hottest shows on Yahoo! TV. http://tv.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs result
Dear all I have 3 complexes of docking.(one receptor with 3 different ligands).I studied MD of 3 complexes in 15 ns by gromacs.how can i compare binding energy and affinity of 3 ligands with receptor.(how can i analysis gromacs result) thanks Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545469 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] translate
Dear all i want to translate the protein coordinates to center of the hole in membrane(i want to insert protein in membrane).how can i do it with editconf. thanks Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase. http://farechase.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] center of mass
Dear all i want to determine the center of mass of my protein in the z-dimension.which command in gromacs is useful for me? thanks Choose the right car based on your needs. Check out Yahoo! Autos new Car Finder tool. http://autos.yahoo.com/carfinder/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] make-hole,grasp
Dear all I want to make hole in popc. i prepared the grasp molecular surface . how can i use grasp result in run make-hole. thanks Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545469 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] linux
Dear all I have a problem in linux: When I attempt to log in as root i'm seeing the following error directly after entering the password and username. "Your session only lasted less that ten seconds. If you have not logged out yourself, this could mean that there is some installation problem or that you may be out of diskspace. Try logging in with one of the failsafe sessions to see if you can fix the problem" thanks Building a website is a piece of cake. Yahoo! Small Business gives you all the tools to get online. http://smallbusiness.yahoo.com/webhosting ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] make-hole
Dear all I want to insert protein in bilayer. in make-hole program, what is -r -cx and -cy ? how can i select them?(they are grasp result or no) best regards Building a website is a piece of cake. Yahoo! Small Business gives you all the tools to get online. http://smallbusiness.yahoo.com/webhosting ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] protein in hole
Dear all i want to insert potassium channel in popc, i made popc+hole by make-hole but i can not to insert protein in popc, i merg the coordinates of the protein and the lipid bilayer in a single file, the protein turns out not to be inside the hole. I have to orient the protein so that the channel axis coincides with the membrane normal.how can i do it by editconf or grasp? thanks Ready for the edge of your seat? Check out tonight's top picks on Yahoo! TV. http://tv.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] make-hole
Dear all I want to make hole in center of popc bilayer . how can i do it by make-hole program?(cx,cy=?) thanks 8:00? 8:25? 8:40? Find a flick in no time with the Yahoo! Search movie showtime shortcut. http://tools.search.yahoo.com/shortcuts/#news ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] position by editconf
dear all I want to insert protein in bilayer. how can i put position of protein in x,y, and z ralative to the bilayer by editconf? best regards No need to miss a message. Get email on-the-go with Yahoo! Mail for Mobile. Get started. http://mobile.yahoo.com/mail ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein in hole
dear david how can i do by editconf?whould you please help in detail? --- David van der Spoel <[EMAIL PROTECTED]> wrote: > mahbubeh zarrabi wrote: > > dear freinds > > I have made a hole in POPC128a bilayer and did > mdrun > > for popc(make-hole).i merged protein and popc by > cat > > command but protein did not put in hole in > popc.whould > > you please help me? > > thanks > > > start with > man cat > you could try by centering the hole and the protein > on te same point > with editconf and then merge them using a text > editor > > > > > > > > > > Be a better Globetrotter. Get better travel > answers from someone who knows. Yahoo! Answers - > Check it out. > > > http://answers.yahoo.com/dir/?link=list&sid=396545469 > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the > list. Use the > > www interface or send it to > [EMAIL PROTECTED] > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > -- > David. > > David van der Spoel, PhD, Assoc. Prof., Molecular > Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala > University. > Husargatan 3, Box 596,75124 Uppsala, Sweden > phone:46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] > http://folding.bmc.uu.se > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge to see what's on, when. http://tv.yahoo.com/collections/222 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] protein in hole
dear freinds I have made a hole in POPC128a bilayer and did mdrun for popc(make-hole).i merged protein and popc by cat command but protein did not put in hole in popc.whould you please help me? thanks Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545469 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] editconf (protein+bilayer)
Dear all I have a pdb of my protein. I want to position of protein in x,y and z relative to the bilayer .how can i do by editconf? rhanks Shape Yahoo! in your own image. Join our Network Research Panel today! http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] popc.itp
Dear all I have tried to use popc.pdb that the coordinates are from Tieleman's web to insert a protein in popc.which force field is suitable for it?(popc.itp or...) thanks Need a vacation? Get great deals to amazing places on Yahoo! Travel. http://travel.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp popc
Dear all I am trying to run a simulation of a protein in popc.I run grompp, there is error : atomtype HC not found.where is wrong? itp or top files. thanks Ready for the edge of your seat? Check out tonight's top picks on Yahoo! TV. http://tv.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] simulation popc
Dear yang thanks very much.the some of atomes do not found(NR,CH,N5,...).they are in lipid.itp best wishes --- Yang Ye <[EMAIL PROTECTED]> wrote: > You shall read up manual for the structure of > topology file. > > For your problem, you shall create a top file which > contains > > #include "ffgmx.itp" > #include "lipid.itp" > #include "popc.itp" > #include "prox.itp" > #ifdef POSRES > ; #include "prox-posre-10.itp" > #include "prox-posre.itp" > #endif > #include "spc.itp" > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcxfcyfcz >11 1000 1000 1000 > #endif > ; Include generic topology for ions > #include "ions.itp" > [ system ] > ; Name > protein and POPC > [ molecules ] > ; Compound#mols > Protein_X1 > POP 489 > > Regards, > Yang Ye > > - Original Message > From: mahbubeh zarrabi <[EMAIL PROTECTED]> > To: Yang Ye <[EMAIL PROTECTED]>; Discussion list > for GROMACS users > Sent: Monday, May 28, 2007 7:56:23 PM > Subject: Re: [gmx-users] simulation popc > > > dear freind > thanks for helping. there is another errore: no such > moleculetype protein. > best wishes > --- Yang Ye <[EMAIL PROTECTED]> wrote: > > > Put two semicolon before > > > > ;[ defaults ] > > ;1 1 > > > > in the lipid.itp > > > > - Original Message > > From: mahbubeh zarrabi <[EMAIL PROTECTED]> > > To: gmx-users@gromacs.org > > Sent: Monday, May 28, 2007 4:41:19 PM > > Subject: [gmx-users] simulation popc > > > > > > Dear all > > I want to simulate protein in popc.I dowanload > > popc128a.pdb from tieleman site and insert protein > > in > > popc by VMD BUT I can not run grompp.there is > > errore: > > found a second defaults directive file ffgmx.itp > > line6.whould you please help me?which protocole is > > useful for me(in detail)? > > best regard > > > > > > > > > > > > > Bored stiff? Loosen up... > > Download and play hundreds of games for free on > > Yahoo! Games. > > http://games.yahoo.com/games/front > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the > > list. Use the > > www interface or send it to > > [EMAIL PROTECTED] > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php> > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the > > list. Use the > > www interface or send it to > > [EMAIL PROTECTED] > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > > > > Need Mail bonding? > Go to the Yahoo! Mail Q&A for great tips from Yahoo! > Answers users. > http://answers.yahoo.com/dir/?link=list&sid=396546091> ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Luggage? GPS? Comic books? Check out fitting gifts for grads at Yahoo! Search http://search.yahoo.com/search?fr=oni_on_mail&p=graduation+gifts&cs=bz ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] simulation popc
dear freind thanks for helping. there is another errore: no such moleculetype protein. best wishes --- Yang Ye <[EMAIL PROTECTED]> wrote: > Put two semicolon before > > ;[ defaults ] > ;1 1 > > in the lipid.itp > > - Original Message > From: mahbubeh zarrabi <[EMAIL PROTECTED]> > To: gmx-users@gromacs.org > Sent: Monday, May 28, 2007 4:41:19 PM > Subject: [gmx-users] simulation popc > > > Dear all > I want to simulate protein in popc.I dowanload > popc128a.pdb from tieleman site and insert protein > in > popc by VMD BUT I can not run grompp.there is > errore: > found a second defaults directive file ffgmx.itp > line6.whould you please help me?which protocole is > useful for me(in detail)? > best regard > > > > > > Bored stiff? Loosen up... > Download and play hundreds of games for free on > Yahoo! Games. > http://games.yahoo.com/games/front > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php> ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Need Mail bonding? Go to the Yahoo! Mail Q&A for great tips from Yahoo! Answers users. http://answers.yahoo.com/dir/?link=list&sid=396546091 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] simulation popc
Dear all I want to simulate protein in popc.I dowanload popc128a.pdb from tieleman site and insert protein in popc by VMD BUT I can not run grompp.there is errore: found a second defaults directive file ffgmx.itp line6.whould you please help me?which protocole is useful for me(in detail)? best regard Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. http://games.yahoo.com/games/front ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] atom type not found error
Hello everybody; when I try to create the .tpr file from my .gro and .top files, using command "grompp", there is an error saying atomtype (e.g. OS) not found. when I look at the .atp file at gromacs directory,the atom types and their corresponding masses exist there.what could be the problem and how can I solve it? thank you in advance Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge to see what's on, when. http://tv.yahoo.com/collections/222 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] top
Dear all how can i create popc.top after run make-hole? Got a little couch potato? Check out fun summer activities for kids. http://search.yahoo.com/search?fr=oni_on_mail&p=summer+activities+for+kids&cs=bz ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] protein in popc
Dear all I have made a hole in POPC128a bilayer(make_hole).how can i insert protein into the hole? thanks Pinpoint customers who are looking for what you sell. http://searchmarketing.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energy
Dear all I am trying to calculate the binding free energy of protein and ligand, I used the g_lie command but lie.xvg=0 .what is wrong? thanks Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_energy
Dear GROMACS users I want to calculate free energy in complex,receptor and ligand .what are energy groups in md.mdp? protein,solution or protein,protein,solution thanks Expecting? Get great news right away with email Auto-Check. Try the Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/newmail_tools.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_mindist
Dear all I want to analyze the electrostatic interaction in md.I used g_mindist . in this command how can i select distsnce for contact(-d)? thanks Sucker-punch spam with award-winning protection. Try the free Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/features_spam.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_energy
Dear all I want to calculate binding energy between of ligand and receptor in complex file.how can i describ energy groups in mdp file. best regards Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_energy
Dear all I want to calculate binding energy between of ligand and receptor in complex file.how can i describ gqroups in mdp file. best regards Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energy
Dear all how can I calculate interaction energy in complex with gromacs best wishes Need a quick answer? Get one in minutes from people who know. Ask your question on www.Answers.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to restrain the atom position/distance in one molecule?
Hi all, I am going to run a MD for a multi-subunit channel.I want to fix a part of the molecule,e.g. by keeping the distance between two atoms in two separate subunits, so that those parts do not move apart from eachother.clearly,I want to keep the subunits on their initial positions as much as possible,but I dont know how to do it initialy.where and how should I add parameters to my file? can any one give a suggestion or an example of a file containing similiar input? I will appreciate it. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_potential
Dear user How can I calculate electrostatic potential in md time? what is index file in g_potential? thanks __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] contact
Dear freinds I want to analyz the formed contact in during the MD.How can i do with gromacs? best regard __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein in bilayer
dear itamar where is adress make-hole site? thanks __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] protein in bilayer
Dear freinds I want to insert protein (K channel) in bilayer lipid.whould you please help me? best regard __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] editconf
Dear gmx_users I am trying to insert one channel peptide in lipid bilayer. I created two pdbs, bilayer.pdb and peptide.pdb . how can i were adjusted the peptide coordinates using editconf to be at the desired vertical position in the bilayer. thanks __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] editconf
Dear gmx_users I am trying to insert one alpha-helical peptide . I created two pdbs, bilayer.pdb and peptide.pdb . how can i were adjusted the peptide coordinates using editconf to be at the desired vertical position in the bilayer. thanks __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] contact
Dear gromacs users How can i calculate the number of contacts during the MD trajectory in complex(protein-protein)? best regard __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_sas
Dear all how can i compute solvent accessible surface area for a special residue in all of time? thanks __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] electostatic
Dear freinds can i study electrostatic interactions in complex by gromacs? how?whould you please help me? thanks __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] make_hole
Dear freinds I want to make a hole in popc , i run below commands make_hole.pl -f .pdb -o .pdb -r 2.7 -lipat p8 -lipid pop grompp_hole -f .mdp -o .tpr -c .pdb -r .pdb -p .top but error is appear: one of the box vectors is shorter than twice the cut_off lenght. whould you please help me? best regard __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] channel in popc
Hi freinds I try to use make_hole program to make a hole in popc and input ion channel in it.whould you please help me? mahbubeh __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] channel in popc
hi freinds I try to use make_hole program to make a hole in popc and input ion channel into it.whould you please help me ? mahboobeh __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] insertion
Dear freinds how can i put protein file in popc(has hole)file? how can i combine the protein and popc? thanks zarrabi __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] protein in popc
dear freinds I have made a hole in POPC128a bilayer.But I failed inputing protein into it.I run below commands but there is not protein in the hole.whould you please help me? do you have another protocol for protein insertion in popc (in detail)? make_hole.pl -f popc.pdb -o popcout.pdb -r 1.4 -lipat P8 -lipid POP -cx 2.3 -cy 2.8 grompp -f run.mdp -o insert.tpr -c popcout.pdb -p popc.top mdrun -v -hole -holep hp.mdp -deffnm insert - popc.top is here: ; Topology for a pure POPC bilayer with 106 lipids and 2460 water molecules #include "ffgmx.itp" ; #include "lipid.itp" #include "popc.itp" #ifdefFLEX_SPC #include "flexspc.itp" #else #include "spc.itp" #endif [ system ] ; name Pure POPC bilayer with 106 lipids and 2460 water molecules [ molecules ] ; name number POPC 106 SOL2460 -- popc.mdp is here : ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = POPC128a cpp= /lib/cpp define = -DPOSRES -DFLEX_SPC dt = 0.002 ; ps! nsteps = 5 ; total 10 ns. nstcomm= 1 integrator = md ; Output control nstxout= 5000 nstvout= 5000 nstfout= 0 nstlog = 5000 nstenergy = 5000 ; Neighbor searching nstlist= 10 ns_type= grid rlist = 1.0 pbc= xyz ; Bonds constraints= all-bonds constraints_algorithms = lincs unconstrained_start= no lincs_order= 4 lincs_iter = 1 lincs_warnangle= 30 ; Electrostatics and VdW coulombtype= PME rcoulomb = 1.0 rvdw = 1.0 fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = POPC SOL tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = POPC SOL ; Pressure coupling Pcoupl = berendsen pcoupltype = isotropic tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 -- hp.mdp is here: holetype = MSMS hfm = 10 supf = 10 molsurf_log = gsurf.log hr = 0 hx = 0 hy = 0 hz = 5.0 hp1 = 1 hp2 = 2120 s1 = 0 s2 = 0 hz1 = 3.3 hz2 = 7.3 sfm = 10.0 sofs = 0.15 molsurf_file = /home/zarrabi/msms/com18 debugsurf= no resforces= yes -- best regards zarrabi __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] protein in popc
I have made a hole in POPC128a bilayer.But I failed inputing protein into it.I run below commands but there is not protein in the hole.whould you please help me? do you have another protocol for protein insertion in popc (in detail)? make_hole.pl -f popc.pdb -o popcout.pdb -r 1.4 -lipat P8 -lipid POP -cx 2.3 -cy 2.8 grompp -f run.mdp -o insert.tpr -c popcout.pdb -p popc.top mdrun -v -hole -holep hp.mdp -deffnm insert - popc.top is here: ; Topology for a pure POPC bilayer with 106 lipids and 2460 water molecules #include "ffgmx.itp" ; #include "lipid.itp" #include "popc.itp" #ifdefFLEX_SPC #include "flexspc.itp" #else #include "spc.itp" #endif [ system ] ; name Pure POPC bilayer with 106 lipids and 2460 water molecules [ molecules ] ; name number POPC 106 SOL2460 -- popc.mdp is here : ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = POPC128a cpp= /lib/cpp define = -DPOSRES -DFLEX_SPC dt = 0.002 ; ps! nsteps = 5 ; total 10 ns. nstcomm= 1 integrator = md ; Output control nstxout= 5000 nstvout= 5000 nstfout= 0 nstlog = 5000 nstenergy = 5000 ; Neighbor searching nstlist= 10 ns_type= grid rlist = 1.0 pbc= xyz ; Bonds constraints= all-bonds constraints_algorithms = lincs unconstrained_start= no lincs_order= 4 lincs_iter = 1 lincs_warnangle= 30 ; Electrostatics and VdW coulombtype= PME rcoulomb = 1.0 rvdw = 1.0 fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = POPC SOL tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = POPC SOL ; Pressure coupling Pcoupl = berendsen pcoupltype = isotropic tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 -- hp.mdp is here: holetype = MSMS hfm = 10 supf = 10 molsurf_log = gsurf.log hr = 0 hx = 0 hy = 0 hz = 5.0 hp1 = 1 hp2 = 2120 s1 = 0 s2 = 0 hz1 = 3.3 hz2 = 7.3 sfm = 10.0 sofs = 0.15 molsurf_file = /home/zarrabi/msms/com18 debugsurf= no resforces= yes -- best regards zarrabi __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] protein insertion
Dear freinds I want to make hole in popc and insert protein in lipid. I do all steps but I do not know when i use below command , what is happend? mdrun -v -hole -holep hp.mdp -deffnm insert ... what is outfile? how can i insert protein in popc? sincerely yours zarrabi __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] atomtype
Hi,everyone, I have tried to use popc.pdb that the coordinates are from Tieleman's web to insert a protein.when i use ffgmx.itp , there is fetal error: atomtype LC3 not found. i downloaded ffgmx_lipid but i have a problem: fetal error: invalid order for directive atomtypes file .share\top\... line 1 whould you please help me? best regards zarrabi __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] popc
hi I try to use make_hole program to make a hole in POPC. how can i make popc.top?what is forcefield for popc in gromacs? thanks zarrabi __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] top file popc
hi i run pdbgmx2 for popc but errore message is here: wrong format is in ffg43a2.h line 2 7 ow whould you please help me? thanks mahboobeh __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] protein insertion
Dear freinds There are some errors when I run grompp. I try to use make_hole program to make a hole in POPC. ./make_hole.pl -f popc128a.pdb -o popc.pdb -r 1.4 -lipat P8 -lipid POPC -cx 2.3 -cy 2.8 editconf -f popc.pdb -o popc.gro editconf -bt cubic -f popc.gro -o popc.gro -c -d 0.5 genbox -cp popc.gro -cs spc216.gro -o popc_b4em.gro -p popc.top This is my popc.top after genbox. #include "ffgmx_lipid.itp" #include "popc.itp" ;#include "ions.itp" #ifdef POSRES #include "lipid_posre.itp" #endif #ifdef FLEX_SPC #include "flexspc.itp" #else #include "spc.itp" #endif [ system ] ; name popc + h2o [ molecules ] ; name number POPC 106 There is my em.mdp file. cpp = /lib/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no grompp -f em.mdp -c popc_b4em.gro -p popc.top -o popc.tpr After doing these, error message is appeare: popc.top:1:27: error: ffgmx_lipid.itp: No such file or directory popc.top:2:20: error: popc.itp: No such file or directory cpp exit code: 256 Tried to execute: '/lib/cpp -I/usr/local/gromacs/share/top -DFLEX_SPC popc.top > gromppzaUDO1' The '/lib/cpp' command is defined in the .mdp file processing topology... Cleaning up temporary file gromppzaUDO1 --- Program grompp, VERSION 3.3.1 Source code file: topio.c, line: 388 Fatal error: Invalid order for directive moleculetype, file ""/usr/local/gromacs/share/top/flexspc.itp"", line 1 best regard zarrabi __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
