Re: [gmx-users] simulation of protein in popc box

Hello Shamik, Going through the membrane protein tutorial will help you to get answers to these questions. The lipid.itp file has to be modified and edited depending on the force fields being used like opls force field or the gromos96 force field. Popc.itp file should also be included in order to

Re: [gmx-users] simulation of protein in popc box

Hello, Greetings from Pawan. Topologies for lipids like POP are not available in the topology database in gromacs. So the starting point would be to generate a topology and a gro file for the protein alone as such and then edit the topology to include the .itp files as specifically needed for the

Re: [gmx-users] problem with system neutralization

genion.log is still -4! > > Why? > > Cheers, > > Stefano > > > Pawan Kumar ha scritto: > >> Hello, >> >> Greetings from Pawan. >> -np is a parameter used to add the nmber of positive ions. >> when u have -4 negative charge u should give -n

Re: [gmx-users] problem with system neutralization

Hello, Greetings from Pawan. -np is a parameter used to add the nmber of positive ions. when u have -4 negative charge u should give -np 4. -np with -pname will be more appropriate. see through this website for the proper usage of genion options. http://www.gromacs.org/documentation/reference_3.3/

Re: [gmx-users] How to remove water from lipid bilayer core

Hello Anirban, Greetings from Pawan. You can find the scripts in this webiste : http://wiki.gromacs.org/index.php/Membrane_Simulations Regards, Pawan On Thu, May 14, 2009 at 3:01 PM, Anirban Ghosh wrote: > Hi ALL, > > I have a built a system of protein embeded in lipid bilayer and solvated it >

Re: [gmx-users] Re: Problem with protein in lipid bilayer simulation

Hello Anirban, This is due to some wrong editing and modifications of the .itp files. Please follow the tutorial carefully. The explanation for each modification is also given quite clearly. Regards, Pawan On Tue, May 12, 2009 at 2:26 PM, Anirban Ghosh wrote: > Hello Pawan and Justin, > > Thank

Re: [gmx-users] Re: Problem with protein in lipid bilayer simulation

Hi Anirban, I have also followed Justin sir's tutorial. You should not remove the OW entries. You can remove the HW entries for sure and then this will work. Regards, Pawan On Tue, May 12, 2009 at 9:45 AM, Anirban Ghosh wrote: > Hello Justin, > > Thanks a lot for the reply. Your tutorial is ind

Re: [gmx-users] protein falls apart in energy minimization

hi, Defining a specific box size with -d option in editconf will help to overcome this problem... Regards, Pawan On Tue, May 12, 2009 at 8:05 AM, Zhong Zheng wrote: > hi all > > I am running Gromacs on a protein consisted of three chains. But no matter > how I tried, the protein always falls i

Re: [gmx-users] Warning: Pressure scaling more than 1%.

Hi, Increasing the tau-p value in the parameter file should help. Regards, Pawan On Mon, May 11, 2009 at 11:06 AM, Zhanglin Ni wrote: > Dear all, > when I run position-restrained simulation (total 15000steps). when it > reached 740 steps > Step 741 Warning: Pressure scaling more than 1%. > >

Re: [gmx-users] problem with genion

Use solvent group (Group 13) for neutralization. Pawan On Sat, May 9, 2009 at 5:03 PM, nitu sharma wrote: > Dear all, > >Thanks for solving lot of problem of me in doing > membrane membrane protein simulation. Now I have a one problem I want to add > ion to the my system by

Re: [gmx-users] energy xvg file shows a large energy change from time step 0 to time step 0.2 ps

hi, It will be better to check the energy after the final production run Pawan On Fri, May 1, 2009 at 12:15 AM, Halie Shah wrote: > > Hi! > > I have just completed a position restrained dynamics run on my protein with > GROMACS 3.3.3 and I generated an xvg file with the g_energy command..

Re: [gmx-users] mdrun error

probably a bad starting structure... check this website for pressure scaling warning : http://wiki.gromacs.org/index.php/Errors regards, pawan On Mon, Apr 27, 2009 at 5:21 PM, Sheetal Arora wrote: > I am trying to run the simulation of protein ligand complex. > But after running the mdrun by gi

Re: [gmx-users] problem in energy minimisation

On Fri, Apr 24, 2009 at 4:13 PM, nitu sharma wrote: > Dear Mark > > After doing second step of inflategro i.e compression step when I > did the enery minimisation with nstep-1 in parameter file it > terminated after 1547 steps and written that - > Converged to machine precision, >

Re: [gmx-users] Membrane protein tutorial

PM, Justin A. Lemkul wrote: > > > Pawan Kumar wrote: > >> Hello Sir, >> >> The whole point in making an index file was to merge the sol and cl- ions. >> If i put popc also in the index file then it wont make any much useful >> group because lipids needs to

Re: [gmx-users] Re: Membrane protein tutoria

Thanks for your mail sir. I will do some reading as per your suggestion. On Thu, Apr 9, 2009 at 10:45 AM, wrote: > Dear Pawan, > > I suggest that you try doing some protein in water simulations or some > available tutorials before you proceed with your bilayer study. You might > also consider re

Re: [gmx-users] Membrane protein tutorial

at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Thanking you, Pawan On Thu, Apr 9, 2009 at 10:38 AM, Mark Abraham wrote: > Pawan Kumar wrote: > >> Hello Mark Sir, >> >> I have tried that way also. >> The command

Re: [gmx-users] pdb file and force filed

Hello, For usual peptides having amino acids you need not use Dundee Prodrg server. pdb2gmx itself will generate the required .itp and .gro files. If u were using opls force fiels in tinker then use the same force fields in gromacs also because atom types are defined in different ways in different

Re: [gmx-users] Membrane protein tutorial

9903 9167 > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > -- > *From:* gmx-users-boun...@gromacs.org [mailto: > gmx-users-boun...@gromacs.org] *On Behalf Of *Pawan Kumar

Re: [gmx-users] Membrane protein tutorial

Apr 9, 2009 at 10:14 AM, Mark Abraham wrote: > Pawan Kumar wrote: > >> Hello sir, >> >> Thanks for such a explanatory tutorial. >> I am stuck with one error now. >> I have protein, popc, sol and cl- in my system. >> I have merged the sol and cl- using make

Re: [gmx-users] Membrane protein tutorial

Hello sir, Thanks for such a explanatory tutorial. I am stuck with one error now. I have protein, popc, sol and cl- in my system. I have merged the sol and cl- using make_ndx. But when I run grompp I get the error like this "popc not defined in the index file". The grompp command : grompp -f pr.md

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Sir, Thanks for your mail. I will work on this. Thanking you, Pawan On 4/7/09, Mark Abraham wrote: > > Pawan Kumar wrote: > >> Hello Sir, >> >> Can you please tell me how to couple ions with SOL ? >> Is there any command in gromacs to do that ? >&

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Hello Sir, Can you please tell me how to couple ions with SOL ? Is there any command in gromacs to do that ? Thanking you, Pawan On Tue, Apr 7, 2009 at 9:44 AM, Mark Abraham wrote: > Pawan Kumar wrote: > >> Respected Sir, >> >> Greetings from Pawan. >> Sorry f

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Pcoupl_type = semiisotropic ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Thanking you, Yours sincerely, Pawan On Mon, Apr 6, 2009 at 5:35 PM, Justin A. Lemkul wrote: > > > Pawan Kumar wrote: > >>

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Sir, Greetings from Pawan. > 1. Were there gaps between the water and lipid headgroups? If so, the > lipids may be pulling towards the solvent. Restrain the lipids and run an > equilibration for a longer time. Gap was there when I used a value of 0.5 in the vdwradii.dat file. The

Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

move apart > during MD ? > > Definetly you should perform another position restraint MD, restraining the > protein only. > > Andreas > > >>>>>>>>>>>>>>>> > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromac

[gmx-users] Doubt regarding membrane protein in POPC bilayer

rom: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Pawan Kumar > Sent: 06 April 2009 07:47 > To: Discussion list for GROMACS users; jalem...@vt.edu > Subject: [gmx-users] Doubt regarding membrane protein in POPC bilayer > > Respected Sir, > > Gre

Re: [gmx-users] NEUTRALISED CHARGES

Hi, You should add 14 cl ions. Regards, Pawan On Mon, Apr 6, 2009 at 12:26 PM, akalabya bissoyi < bissoyi.akala...@gmail.com> wrote: > hello gromacs > i am trying to minimise my protein-ligand complex in gromacs.but it shows > that system has non zero charge > can any body says how much *cl ion

[gmx-users] Doubt regarding membrane protein in POPC bilayer

quite acceptable as the lipids have pulled apart and there is a huge gap between the two layers of the lipids. I have made the run for 5000 steps with dt = 0.002. Any suggestions please. Thanking you, Yours sincerely, Pawan On Tue, Mar 31, 2009 at 5:50 PM, Justin A. Lemkul wrote: > > &

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Sir, Greetings from Pawan. Thanks for your information. Thanking you, Pawan On Tue, Mar 31, 2009 at 5:50 PM, Justin A. Lemkul wrote: > > > Pawan Kumar wrote: > >> Respected Sir, >> >> Greetings from Pawan. >> Thanks for all your kind help and

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Marc Sir, Thanks for your information. Thanking you, Pawan On Tue, Mar 31, 2009 at 5:31 PM, Marc F. Lensink wrote: > On Tue, Mar 31, 2009 at 07:23:57AM -0400, Justin A. Lemkul wrote: > > > > Force fields have to be internally self-consistent, so using the > parameters > > from OPLS wi

[gmx-users] Doubt regarding membrane protein in POPC bilayer

hydrophobic part of the bilayer ? Thanking you, Yours sincerely, Pawan On Tue, Mar 31, 2009 at 5:31 PM, Justin A. Lemkul wrote: > > > Pawan Kumar wrote: > >> Respected Sir, >> >> Greetings from Pawan. >> Thanks for all your suggestions. >> Is it possible to

[gmx-users] Doubt regarding membrane protein in POPC bilayer

using ? I am sorry to ask this but can you please help me with some information how to modify the lipid.itp file ? I will edit vdwradii.dat file as per your suggestion. Thanking you, Yours sincerely, Pawan On Tue, Mar 31, 2009 at 4:53 PM, Justin A. Lemkul wrote: > > > Pawan Kumar wrote:

[gmx-users] Doubt regarding membrane protein in POPC bilayer

omp_em27.pdb -cs spc216.gro -o box.pdb -p topol.top Thanking you, Yours sincerely, Pawan On Tue, Mar 31, 2009 at 4:20 PM, Justin A. Lemkul wrote: > > > Justin A. Lemkul wrote: > >> >> >> Pawan Kumar wrote: >> >>> Respected Sir, >>> >>&g

Re: [gmx-users] problem in simulation of lipid bilayer

Dear Nitu madam, You can directly go for simulation of lipid+protein complex if u r using a pre-equilibrated bilayer as from Dr. Tieleman's website. Regards, Pawan 2009/3/31 nitu sharma > Dear all, > > I am trying to simulation of membrane proteins I have a > basic question

[gmx-users] Doubt regarding membrane protein in POPC bilayer

1 Protein_B 1 Protein_C 1 DPPC 926 ;SOL 23552 Please help with some suggestions. Thanking you, Yours sincerely, Pawan On Mon, Mar 30, 2009 at 6:22 PM, Justin A. Lemkul wrote: > Pawan Kumar wrote: > >> Respected Sir, >> >&

[gmx-users] Doubt regarding membrane protein in POPC bilayer

gs and Segementation fault after few steps (30 - 40 steps). Can you please help how to proceed ? Thanking you, Yours sincerely, Pawan On Mon, Mar 23, 2009 at 6:26 PM, Justin A. Lemkul wrote: > > > Pawan Kumar wrote: > >> >> Respected Sir, >> >> Greetings fro

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

Hello Madam, Greetings from Pawan. The solution for this is to edit the atom names as required such as replace NTM with N4 in all the places wherever NTM occurs. Similarly do this for all the atoms of the dppc lipid. I think this is a probable solution. I dont know how far I am right. Regards, P

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

Hi, Greetings from Pawan. Edit your lipid.itp file. Comment or remove the lines : [default] 1 1 Then grompp will work.. Regards, Pawan 2009/3/30 nitu sharma > Dear all , > > > I am trying to do simulation of DMPC lipid > bilayer for this I

[gmx-users] Doubt regarding membrane protein in POPC bilayer

: > > > Pawan Kumar wrote: > >> >> Respected Sir, >> >> Greetings from Pawan. >> I read in the manual about the freeze-grps but dint find a good >> explanation about the usage. >> Can you please tell me how to use freeze-grps in all dimensions d

[gmx-users] Doubt regarding membrane protein in POPC bilayer

kul wrote: > > > Pawan Kumar wrote: > >> Respected Sir, >> >> Thanks for all your help, suggestions and guidance. >> I have few more queries. >> Which type of box is appropriate in editconf - cubic or triclinic ? >> > > That depends entirely upo

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Respected Sir, Thanks for all your help. I will try this out and if I have any further queries I will ask you. Thanks a lot. Thanking you, Pawan On Mon, Mar 23, 2009 at 5:58 PM, Justin A. Lemkul wrote: Pawan Kumar wrote: > Respected Sir, > > Thanks for all your help, sugges

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Sir, Thanks for all your help, suggestions and guidance. I have few more queries. Which type of box is appropriate in editconf - cubic or triclinic ? I have read in one of your mails in the archives that POPE bilayer contains some bad interactions. As it contains more no. of lipids (340)

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Is it fine if I generate the .gro files using editconf command ? Thanks for your kind help. Thanking you, Pawan On Mon, Mar 23, 2009 at 5:02 PM, Justin A. Lemkul wrote: > > > Pawan Kumar wrote: > >> Respected Sir, >> >> Greetings from Pawan. >> Thanks for y

[gmx-users] Doubt regarding membrane protein in POPC bilayer

: > > > Pawan Kumar wrote: > >> Hello Justin Sir, >> >> Greetings from Pawan. >> Sorry for the inconvenience. >> Next time I will keep in mind about the subject line. >> I tried deleting those particular atoms where it gave the maximum force. >> >

[gmx-users] Doubt regarding membrane protein in POPC bilayer

"constraints = all-angles" in order to overcome the Lincs warnings ? Thanks in advance. Thanking you, Pawan On Mon, Mar 23, 2009 at 4:16 PM, Justin A. Lemkul wrote: > > When replying to digests, please change the subject line to something > relevant. > > Pawan Kumar wro

Re: [gmx-users] Re: gmx-users Digest, Vol 59, Issue 138

at 6:08 PM, Justin A. Lemkul wrote: > > > Pawan Kumar wrote: > >> Hello Justin Sir, >> >> Greetings from Pawan >> Thanks for your valuable suggestion and reply. >> Initially I gave the emtol of 1000 and the output I got was : >> Steepest Descents

[gmx-users] Re: gmx-users Digest, Vol 59, Issue 138

, Pawan On Thu, Mar 19, 2009 at 9:13 PM, > Pawan Kumar wrote: > > Hello Justin Sir, > > > > Greetings from Pawan > > Thanks for your valuable suggestion and reply. > > After inserting the protein in the bilayer using genbox I have minimized > > the whole

Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

here any parameter to be given in the em.mdp file ? I use steep as the integrator in the mdp file for energy minimization. Please help with some suggestions. Thanks in advance. Thanking you, Pawan On Thu, Mar 19, 2009 at 5:41 PM, > Pawan Kumar wrote: > > Hello Justin Sir, > > > >

Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

before. One last question is how to overcome the lincs warnings in position restraint mdrun. Thanks in advance. Thanking you, Pawan On Thu, Mar 19, 2009 at 5:01 PM, > Pawan Kumar wrote: > > Hi Xavier sir, > > > > Thanks for your valuable reply. > > How can I refine

[gmx-users] Re: gmx-users Digest, Vol 59, Issue 136

before. One last question is how to overcome the lincs warnings in position restraint mdrun. Thanks in advance. Thanking you, Pawan On Thu, Mar 19, 2009 at 5:01 PM, > Pawan Kumar wrote: > > Hi Xavier sir, > > > > Thanks for your valuable reply. > > How can I refine

Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

You can reach the person managing the list at >gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Doubt regarding membrane p

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Dear gmx-users, Greetings from Pawan. I have modelled the structure of a protein using Modeller and then energy minimized using gromacs. Then I used the popc128a bilayer from Tieleman sir's website for inserting the protein. I created a bigger bilayer using the genconf command in gromacs. I was ab