[gmx-users] problem during energy minimisation to allow only hydrogen molecule to relax

-mode = Linear pbc = XYZ Thanks a lot in advance. Nitu sharma. ___ 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

[gmx-users] problem in energy minimisation to allow only hydrogen molecule to relax

- Thanks a lot in advance. Nitu sharma. ___ 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! Please don't post (un)subscribe req

[gmx-users] problem during energy minimisation using cg integrater

= no gen_vel = no comm-mode = Linear pbc = XYZ If anyone have idea regarding this please suggest me to solve this problem for this I will be really thankful to him/her. thanks a lot. nitu sharma ___ gmx-users

[gmx-users] pdb file badly broken after changing residue name a/c to amber.rtp file

Dear justin I am trying to do simulation of dna-protein complex . For this I am using amber port with gromacs-4.0.3 but for this a/c to ffamber.rtp file entry i hqve to make changes in my .pdb file residues like the DNA base name in this is only A ,C ,G,T so a/c to amber.r

[gmx-users] long-bond warning during running

e can I use missing option for further processing . or If it will make harm to simulation process please suggest me something to solve this long bond problem. Thanking you Nitu sharma. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.

[gmx-users] problem in energy minimisation of dna-protein complex

Tcoupl = no Pcoupl = no gen_vel = no comm-mode = Linear pbc = XYZ can anyone suggest how can i get rid from this problem. Thanks a lot in advance. Nitu sharma ___ gmx-users mailing list

[gmx-users] problem during simulation of dna-protein complex

Tcoupl = no Pcoupl = no gen_vel = no comm-mode = Linear pbc = XYZ Specially where i have apply position restrain? Thanking you Nitu sharma ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] problem in simulation of dna-protein complex

6 C3'amber99_110.0713027 H3'amber99_190.0985028 C2'amber99_11 -0.0854029 H2'1amber99_180.0718030 H2'2amber99_180.0718031 O3'amber99_44 -0.5232032 So, can anyone suggest me at the

[gmx-users] problem in dna-protein simulation

- --- Program pdb2gmx, VERSION 4.0.3 Source code file: resall.c, line: 426 Fatal error: Residue 'T' not found in residue topology database Can anyone suggest me how can I overcome this problem . Thanks a lot in advance. Nitu sharma Jawaherlal Nehru

[gmx-users] problem regarding removal of water from final simulation system.

tin,s tutorial also to make final pdb after simulation. So can anyone suggest me how to remove water form my final simulation system to make final pdb of only protein and lipid molecule? If anyone can help me I willbe really thankful for him/her. Nitu Sharma. Jawaherlal Nehru University New

[gmx-users] problem with trjconv

a/c to my opinion in group 0 there may be water also but I want to remove water . so please if anyone have idea about this please suggest me . thanks a lot. Nitu Sharma. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/li

[gmx-users] problem in equilibration step

_temp= 323 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed Thanks a lot in advance. Nitu sharma ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-

[gmx-users] removal of unwanted water from hydrphobic core of lipid

ch in advance. nitu sharma. ___ 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

[gmx-users] problem in neutralising my system

then system still have +3 charge . so please anyone suggest me how much ion will be suitable to neutrilise my system? Thanks a lot . Nitu sharma ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] wrong number of control atoms (3 iso 4) on line

th pdb2gmx command but I am getting error like this - Error in hdb file ffoplsaano.hdb: Wrong number of control atoms (3 iso 4) on line: 1 5 H4* C4* O4* C5* Can anyone suggest me how can I solve this problem? Thank you very much in advance. N

[gmx-users] problem in removal of unwanted water from hydrophobic core of lipid bilayer

_system.gro" ?. Can anyone help me to solve this problem.? I will be really thankful for that. Nitu sharma. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://w

[gmx-users] removal of water from hydrophobic core of lipid

embedded in lipid bilayer. If anyone did these things please help me in solving this problem. I will be really thankful for that. Nitu Sharma School of Life Sciences Jawaherlal Nehru University New delhi , India ___ gmx-users mailing listgmx-users

[gmx-users] problem regarding dna-protein simulation

acid thats why I have left the mail on users list . so If anybody solved this type of problem previously can help me. Thanks a lot. Nitu sharma ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] problem in simulation of dna-protein complex

Idea what short of changes it needed please help me. Thanks a lot in advance. Nitu sharma ___ 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

[gmx-users] problem in DNA simulation

mber of control atoms (2 iso 3) on line: 1 1 N -C CA Can u please help me in solving this problem.? What does mean 2 iso 3? Nitu Sharma ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/g

[gmx-users] problem in simulation of DNA-protein complex

e topology database So , actually I am unable to understand what should I do to solve this . Is it possible to get DNA.itp file from anywhere .If anyone have Idea about this please help me. I really will be very thankful for him/her. Nitu sharma ___

[gmx-users] simulation of DNA model

Dear all I want to ask one basic question i.e is it possible to do simulation of DNA model with gromacs ? If it possible which force field will be suitable for this? I am waiting for yours reply. thanks a lot in advance. Nitu sharma

[gmx-users] lipid_posre.itp file

Dear all I need lipid_posre.itp file can anyone suggest me from where I can find it ?or If I have to make it by my own then please let me know how can I make it. If anyone can suggest me I really will be thankful for him. Nitu Sharma

[gmx-users] problem with genion

a multiple of 8 --- can any suggest me what should I do to solve this problem . I am doing first time all these these things so if anyone can suggest me something I will be really thankful for him/her. Thanks a lot. Nitu Sharma School of life sciences Jawaherlal n

[gmx-users] error during solvation of system

his problem . Is it related with system memory on which i am working or it related with gromacs . If anybody have idea about this please suggest me something. Thank you very much in advance. Nitu Sharma . ___ gmx-users mailing listgmx-users@

[gmx-users] Problem in applying postion restrain on protein

ion specific to this will really helpful for me. Nitu sharma School of Life Sciences Jawaherlal nehru University New Delhi,India ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] problem in applying position restrain on protein

o included- define = -DPOSRES in em.mdp file. also edited posre.itp file with force constant 10. Even after doing these things the restrain not working on protein thats why my protein structure being disturbed . Can any one help me in solving this problem. Thanks a lot in advan

[gmx-users] Steepest Descents converged to machine precision

uot;posre_B.itp #endif But its not working . I am unable to understand why? can u give me some idea about that? NITU sharma ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archi

[gmx-users] Steepest Descents converged to machine precision

120 my question- 1. probable reason of steepest descent converged to macine precision but did not reach the requested Fmax < 1000. 2.The even after applying strong position restrain on protein the protein structure being disturbed. If u can make he

[gmx-users] steepest descents converged to machine precision in several steps.

force constant-10 ,the protein structure being disturbed . Please help me in solving these two problem. THANKS NITU SHARMA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] minimisation converted into machine precision

ode = Linear pbc = XYZ SO please anyone suggest where I am doing fault ? Nitu sharma ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at h

[gmx-users] problem in energy minimisation

88e+02 Can u suggest me probable solution of this problem .I am unable to understand why this problem comes? Thanks a lot Nitu Sharma Structural biology lab School of life Sciences Jawaherlal Nehru University ___ gmx-users mailing listgmx-users@groma

[gmx-users] grompp error

Dear MARK Now the problem of matching of topology file and coordinate file solved but the other two errors come during running grompp in the second step of inflategro . my command line is like this- grompp -f em.mdp -p topolinflate.top -c inflated_system.gro -o inflated-em.tp

[gmx-users] problem in making topology file for protein inlipid bilayer

Dear Mark Thanks for your consideration. I am replying you again I think it will be more easy for u in understanding my problem. as u ask- how many atoms is--Protein A- 5244 Protein B- 4658 And in one dmpc molecule there is 46 atoms so

[gmx-users] Re: gmx-users Digest, Vol 60, Issue 116

.." > > > Today's Topics: > > 1. Re: np command with GROMACS 4.0.4 (Vitaly V. Chaban) > 2. Re: RMSD of Aminoacids (Mark Abraham) > 3. problem in topology file of protein-lipid bilayer system for > grompp (nitu sharma) > 4. validating gromacs install

[gmx-users] problem in topology file of protein-lipid bilayer system for grompp

en't molecules section it have [molecule type ] section can it also create problem for topology file working. Thanks a lot justin . I am waiting for your reply. Nitu sharma School of life sciences Jawaherlal Nehru University New delhi , India ___

[gmx-users] grompp error no. of coordinate file doesn't match with topology file

-- If anyone have idea about this problem please suggest me something to solve this problem. Thnks a lot in advance. Nitu Sharma School of life sciences. Jawaherlal Nehru University New Delhi , India ___ gmx-users mailing listgmx-u

[gmx-users] grompp error no. of coordinate file doesn't match with topology file

-- If anyone have idea about this problem please suggest me something to solve this problem. Thnks a lot in advance. Nitu Sharma School of life sciences. Jawaherlal Nehru University New Delhi , India ___ gmx-users mailing listgmx-u

[gmx-users] problem during inflatgro process

Hi Justin, sorry for disturbing again. But I really need ur help Becoz u already did all these things, I am stucking in inflatgro procedure after step the problem of topology file comes so the energy minimisation step can't be completed- I tell u in detail- after first step I

[gmx-users] problem in energy minimisation during inflategro process.

13253) does not match topology (inflated_dmpc.top, 15395) --- So can you suggest me what possible modification make it successfully completed. please If you have any idea let me know. Thanks a lot justin for solving my problem. Nitu Sharma School of life Sciences Jawahe

[gmx-users] unknown atom type HW

4.0.3 Source code file: toppush.c, line: 618 Fatal error: Unknown atomtype HW Please let me know what possible error give this problem. I have try everything but this problem is still there. Thanks NITU SHARMA SCHOOL OF LIFE SCIENCES JAWAHERLAL NEHRU UNIVERSITY NEW DELHI, INDIA __

[gmx-users] problem in insertion of protein into lipid bilayer in proper orientation

crossing hydrophobic core of lipid . can u suggest me right method to insert my protein into lipidbilayer in proper orientation before using inflategro methedology. I am just stuck on that point . I am eagerly waiting for your reply. Thanks a lot in advance. NITU SHARMA SCHOOL OF LIFE SCIENCES

[gmx-users] problem in increasing lipid bilayer size and to know about net charge on protein

Hi justin Thanks for tutorial of membrane protein simulation its very useful for us . But I want to ask two basic question - 1.The lipid bilayer I have downloded from teleman sir website is so small in comparision with my protein the suitable box vector for my protein is 13nm

[gmx-users] grompp error in simulation of membrane protein.

getting same error . Please Can u suggest me what should I have to do to solve this problem . I am a new gromacs user , I have done the simulation of protein and lipid bilayer separetly but this type of problem didnot came so I have no much idea . I a

[gmx-users] problem in topology file for protein+lipid bilayer system

Hello justin thanks for ur suggestion . I am trying to do membrane protein simulation with lipid bilayer . I have pdb file of inserted protein in dmpc lipid bilayer. But I am facing problem in making topology file for this system.As u told in previous mail you can't combine OPLS_AA with a standerd

[gmx-users] grompp error in running simultion of membrane protein with lipid bilayer

ke this- Program grompp, VERSION 4.0.3 Source code file: toppush.c, line: 843 Fatal error: Atomtype C not found -- my command line like this- grompp -f em.mdp -p rr1-dmpc.top -c solvated-tapp-mod.pdb -o tapp-mod-em.tpr if anyone know about this please suggest me right t

[gmx-users] problem in simulation of lipid bilayer

bilayer . please any one suggest me whats the right thing I have to do. thanks. nitu sharma School of life Sciences Jawaherlal nehru university New delhi,India ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx

[gmx-users] grompp error in running simulation of lipid bilayer

ure all warnings are harmless, use the -maxwarn option. - If u know the solution of this problem please let me know. Thanks in advance. Nitu Sharma School of life sciences Jawaherlal Nehru Univer

[gmx-users] grompp error in running simulation of lipid bilayer

dmpc-em.tpr If anyone know about this please help me in solving this problem . its very useful for me. thank you very much in advance. Nitu Sharma School Of life sciences Jawaherlal Nehru University New Delhi, India ___ gmx-users mailing listgmx-use

[gmx-users] problem in simulation of DMPC lipid bilayer

bilayer from where i can download lipid bilayer then let me know. thanks in advance Nitu Sharma School of life siences Jawaherlal Nehru University New Delhi ,India --- ___ gmx-users maili

[gmx-users] problem in DMPC lipid bilayer

bilayer from where i can download lipid bilayer then let me know. thanks in advance Nitu Sharma School of life siences Jawaherlal Nehru University New Delhi ,India --- ___ gmx-users maili

[gmx-users] nitu sharma has invited you to open a Google mail account

I've been using Gmail and thought you might like to try it out. Here's an invitation to create an account. ------- nitu sharma has invited you to open a free Gmail account. To accept this invitation and register for yo

[gmx-users] problem in running simulation

pdb file -lipid pdb file . what should i have to do next using gromacs. please if anybody knows about that let me know its very critical problem for me. Thank you very much in advance. Nitu Sharma School of life Sciences Jawaherlal Nehru University New Delhi , India

[gmx-users] problem in creating .gro file

plese if possible than anybody help me. Thank you very much for taking out of your time for my consideration. Nitu Sharma Structural Biology lab School Of Life sciences Jawaherlal Nehru University New Delhi, India ___ gmx-users mailing listgmx-users@gro

[gmx-users] problem in creating topol.tpr file

about what problem is existing and what could be the solution of this problem. Thank you very much in advance. Nitu Sharma Structural Biology lab Schoolof life Sciences Jawaherlal nehru university New Delhi, India ___ gmx-users mailing list

[gmx-users] problem in running gromacs demo

l) why the grompp -v terminated even i am going step by step as in mannual. could you please anybody tell me about that. Thank you very much in advance. Nitu sharma Structural Biology lab Schoolof Life Sciences Jawaherlal Nehru University New Delhi,India gmxdump -s topol.tpr | more __

[gmx-users] problem in gromacs installation

ound. Please download and unpack it here.";\ fi) No gmxtest directory found. Please download and unpack it here." This is my second installation why this problem again and again comes . Thank you very much in advance. Nitu Sharma Structural Biology lab School of Life Sc

[gmx-users] problem in running gromacs

but why it shows 3.3.2 and what is the meaning of "File input/output error eiwit.pdb " could you please let me know about that. Thank you very much in advance . Nitu Sharma Structural Biology lab school of life Sciences Jawaherlal nehru university Ne

[gmx-users] problem in running gromacs

bout "can not open file topol.tpr". If anyone has idea about this problem could you please let me know . Thank you very much in advance. Nitu Sharma Structural biology lab School Of life Sciences Jawaherlal Nehru university new delhi, India. ___

[gmx-users] problem in gromacs installation

gment prot after reloc: Permission denied." could you please let me know what exactly the problem is in my installtion and what is the solution of this problem. Thank you very much for taking out your time for my consideration. Nitu Sharma Structural biology lab School of life Sciences

[gmx-users] problem in gromacs installation

s on my linux i686 32 bit system. than you very much in advance. Nitu Sharma Structural Biology Lab Jawaherlal Nehru University New delhi , India ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Ple

[gmx-users] problem in gromacs installation

note on PATH and MANPATH? (I do not have an extensive Linux skills, what file should I modify and how?) Thank you very much in advance Nitu Sharma Structural Biology lab School Of Life Sciences Jawaherlal Nehru University * ___ gmx-users mailing