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 [def

[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 __

[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 custo

[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.y

[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 _

[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

[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

[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 kno

[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 th

[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

[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 chann

[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://

[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

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

[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

[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 to

[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

[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 toni

Re: [gmx-users] simulation popc

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 P

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: m

[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 rega

[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 h

[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=

[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] 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

[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

[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

[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

[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 be

[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] 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 pos

[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] 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 __

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

[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] 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

[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 __ D

[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] 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] 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] 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 re

[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] 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] 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] 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 -li

[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

[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

[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\...

[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] 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] 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 gen