RE: [gmx-users] using xmp file

Hi i found out the residues which form H bond but am still not able to get life time if H bond. The option -lifetime gives t as x and p(t) as y axis. is this value for all the bonds. How can i see the lifetime of each bond? Thanking you pragya chohan > Date: Sat, 3 May 2008 02:06:52 +0

[gmx-users] using xmp file

significance. Can you tell me which files are useful for this purpose? Also please tell me how to visualise xmp files on windows> Thanking You Pragya Chohan _ 2000 Placements last year. Are You next ? Find out http://

[gmx-users] problem with g_order

Dear users I am calculating order parameters of palmitoyl which has 16 carbons. I made the index file with all 16 atoms selected . but the output file has only 14 atoms listed. I have cross-checked the index file. what can be the problem? I am using 3.3 version Thanking you Pragya

[gmx-users] area compressibility modulus

Hi read a paper quoted in the previous post. It calculated area compressibility by : Area compressibility moduli were approximated by using surface tension and APL differencesobtained in simulations. Can anyone please explain what the procedure really is? Thanking You

[gmx-users] request

Dear user Can anyone please send me the below mentioned journal paper "Performance of the general amber force field in modeling aqueous POPC membrane bilayers" thw link is http://www3.interscience.wiley.com/journal/114209721/abstract. Mu institute does not have access. I will be very thankf

[gmx-users] help regarding analysis

hydrophobicity - which I have done 2. some change from helix to coil which I have done through do_dssp Any other suggestion is appreciated Thanking You Pragya Chohan _ Fashion Channel : Want to know what’s the latest in the fashion

RE: [gmx-users] area per lipid

model satisfies all the experimental results before going further. Any suggestion is welcome. > Date: Mon, 28 Apr 2008 22:25:56 -0400> From: [EMAIL PROTECTED]> To: > gmx-users@gromacs.org> Subject: Re: [gmx-users] area per lipid> > Quoting > pragya chohan <[EMAIL PROTECT

[gmx-users] area per lipid

is not equal to 0.658 +/- 0.009. the box-x and box-y are calculated from g_energy. Am I understanding something wrong? Please help Pragya Chohan _ Fashion Channel : Want to know what’s the latest in the fashion world ? You have

[gmx-users] anisotropic coupling tau_p values

s would be appreciated Cheers Pragya Chohan _ Fashion Channel : Want to know what’s the latest in the fashion world ? You have it all here on MSN Fashion. http://lifestyle.in.msn.com/___ gmx-users ma

RE: [gmx-users] Question about different versions of gromacs

hi .. From: [EMAIL PROTECTED]: [EMAIL PROTECTED]: RE: [gmx-users] Question about different versions of gromacsDate: Fri, 28 Mar 2008 12:40:34 +0100 Hi,In minor releases (3.3.?) the tpr file format does not change.Also simulation results should not change, unless a bug was fixed which affec

[gmx-users] lipid parameters for ffG43a1

Pragya Chohan _ Video: Get a glimpse of the latest in Cricket, Bollywood, News and Fashion. Only on MSN videos. http://video.msn.com/?mkt=en-in___ gmx-users mailing listgmx-users

[gmx-users] information about tau_p

Hi users Can you please tell me if in an anisotropic pressure coupling type the diagonal pau_p should be 0 or not. And how it can affect our simulation. What I mean is: I have ref_p = 1.0 1.0 1.0 0 0 0 With that is it better to use tau_p= 1.0 1.0 1.0 0 0 0 or tau_p =1 1 1 1 1 1 and please tel

RE: [gmx-users] understanding of difference between gromacs procedures

f difference between gromacs > procedures > > Quoting pragya chohan <[EMAIL PROTECTED]>: > > > > > the step is indeed equillibration ... thanks for the reply so can we > > say > > that the second step will produce entirely different results throughout

RE: [gmx-users] understanding of difference between gromacs procedures

gmx-users@gromacs.org> Subject: RE: [gmx-users] understanding of difference between gromacs procedures> > Quoting pragya chohan <[EMAIL PROTECTED]>:> > >> > One of my lab-mates> > > > is doing the same system by following a different procedure (difference>

RE: [gmx-users] understanding of difference between gromacs procedures

One of my lab-mates > > is doing the same system by following a different procedure (difference > > listed below) > > I did position restrain by define = -DPOSRES -DPOSRES_LIPID > > and he is doing define = -DPOSRES > > and then for lipid. > > I don't understand what you mean by this. one of

[gmx-users] understanding of difference between gromacs procedures

hello gmx users I am doing a simulation of protein in membrane after simulating a protein in water and inserting it into a membrane. One of my lab-mates is doing the same system by following a different procedure (difference listed below) I did position restrain by define = -DPOSRES -DPOSRES_LIP

RE: [gmx-users] calculating B-factor

thanks for your reply.. but that command gives B-Factor by atom. Is it possible to get by residue... > From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] calculating B-factor> Date: Mon, 18 Feb 2008 12:46:43 +0200> > Hi,> > check out g_rmsf (options -oq, -q, -ox), rmsf

[gmx-users] calculating B-factor

Dear users Is it posible to calculate B-factor for a protein using gromacs? Pragya _ Post free property ads on Yello Classifieds now! www.yello.in http://ss1.richmedia.in/recurl.asp?pid=221_

RE: [gmx-users] fatal error in g_order

o create an index> group that specifies *only* the groups of interest in the index file, i.e. C16,> C17...> > There is a post (I believe from Dallas Warren) that even gives examples of> make_ndx commands to create such groups, if you need that kind of help.> > -Justin>

[gmx-users] fatal error in g_order

hi I am trying to do the bilayer analysis and want to calculate order parameters using g_order. I made the index using make_ndx command and selected the carbons sai 1-16 of my first chain and 17-33 of the other in same index file as two separate group. When I am giving this index file to g_orde

RE: [gmx-users] analysis of POPC

Feb 2008 07:20:54 -0500> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] analysis of POPC> > Quoting pragya chohan <[EMAIL PROTECTED]>:> > >> > hello users> > I am trying to do analysis after bilayer simulation. I cannot get any

[gmx-users] analysis of POPC

hello users I am trying to do analysis after bilayer simulation. I cannot get any experimental data on POPC to validate my model with. Can the people who are working on same lipid tell me some references and also what analysis should be done of the bilayer before putting protein into it? __

[gmx-users] concatenate tpr file

hi users I want todo analysis of my bilayer. So i order to process all trr files I concatenated them with trjcat . Is it also possible to concatenate tpr files in a similar way or I have to fo it imdividually for each trajectory? pragya ___

[gmx-users] information for analysis

hello users please can you tell me how to calculate surface area per lipid, orer parameters, area per head group of lipid from simulation thanks in advance _ Post ads for free - to sell, rent or even buy.www.yello.in http://ss1.richm

[gmx-users] membrane protein simulation

hello users I am starting a membrane protein simulation. I had some missing residues in the protein which have been added now. Should I minimise in vaccum before insertion of the protein in bilayer? Another question : Is it necessary to do simulation in water before inserting protein nto bilay

RE: [gmx-users] problem in bilayer simulation

> I understood that it is a periodic boundry condition problem and used > trjconv. But it writes a trajectory file. How do I make a gro file to > input it into next run Thanks I guess I was wrong. trjconv does write gro files. In any case, working out > how to do the restart is totally separate

RE: [gmx-users] problem in bilayer simulation

my next run? > Date: Mon, 31 Dec 2007 08:17:15 +1100 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] problem in bilayer simulation > > pragya chohan wrote: > > Dear Users > > I am doing membr

RE: [gmx-users] problem in bilayer simulation

can you please suggest what should i do? I have pbc = xyz in my md.mdp> Date: Mon, 31 Dec 2007 08:17:15 +1100> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] problem in bilayer simulation> > pragya chohan wrote:> > Dear Users> >

[gmx-users] problem in bilayer simulation

Dear Users I am doing membrane simulation alternating nvt and npt during production run. After 1250 ps the water from upper leaflet goes towards the lower leaflet and a very thin layer of water remains in the upper leaflet. Is it a common occurance or am I doing some mistake? Please help __

RE: [gmx-users] Segmentation fault

hi generally sementation fault occurs due to bad contacts in the system. As suggested by Mark see if the log file lists atom which have the problem. > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Date: Sat, 29 Dec 2007 17:09:10 +0300 > Subject: [gmx-user

[gmx-users] deleted edr file

Dear users I by mistake deleted the edr file generated from production run. Is there any way to recover or generate the edr file again? _ Post free property ads on Yello Classifieds now! www.yello.in http://ss1.richmedia.in/recurl.

RE: [gmx-users] insert protein in membrane again

Did u match their box size before doing the genbox? You could also get this error if you manually deleted that residue(s) from your gro file. > Date: Tue, 18 Dec 2007 15:29:08 +0100 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-use

RE: [gmx-users] problem with npt

th npt> > Hi,> have you checked if there is no water inside the membrane after the> use of genbox?> > On Dec 16, 2007 1:35 PM, Mark Abraham <[EMAIL PROTECTED]> wrote:> > pragya chohan wrote:> > >> > > i started with the lipid coordinates from peter tiele

[gmx-users] membrane protein

Dear User I am starting a membrane simulation. Is it advisablr to complete all runs in npt or nvt? Pragya Chohan _ Post free property ads on Yello Classifieds now! www.yello.in http://ss1.richmedia.in/recurl.asp?pid

RE: [gmx-users] coupling to water bath

thanks its done. Please read my mail on problem with npt.> Date: Sun, 16 Dec 2007 21:50:33 +1100> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] coupling to water bath> > pragya chohan wrote:> > how can we do that?> > The same way

RE: [gmx-users] coupling to water bath

how can we do that?> Date: Sun, 16 Dec 2007 19:55:30 +1100> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] coupling to water bath> > pragya chohan wrote:> > Dear Users> > I have a system in of protein with in bound chlorine ion.

[gmx-users] coupling to water bath

Dear Users I have a system in of protein with in bound chlorine ion. I also added Na ion to the system to neutralize charge on system. I have to couple the system to water bath. can i couple protein chlorine and Na together and solvent separately? or should i couple protein and chlorine togethe

RE: [gmx-users] problem with npt

bilayers separated and deformed. > Date: Sat, 15 Dec 2007 09:53:06 -0500> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: RE: [gmx-users] problem with npt> > Quoting pragya chohan <[EMAIL PROTECTED]>:> > >> >> > I wrote yes to generate ve

RE: [gmx-users] problem with npt

TECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] problem with npt > > pragya chohan wrote: > > > > thanks for your help. > > My system ran fine for 250 ps but later the bilayer deformed very much. > > What was your system preparation protocol - i

RE: [gmx-users] problem with npt

thanks for your help. My system ran fine for 250 ps but later the bilayer deformed very much. my mdp is integrator = md dt = 0.002; ps ! nsteps = 125000 ; total 100 ps. nstcomm = 1 nstxout = 250 nstenergy = 100 n

[gmx-users] problem with npt

Dear users I was tyring to run an npt simulation of membrane. My mdp is: constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 5 ; total 100 ps. nstcomm = 1 nstxout = 250 nstenergy = 100 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME vdwtype = cut-off ; Berendsen temper

[gmx-users] asymmetric distribution of water

hi ... i want to start a simulation with asymmetric distribution of water on the bilayer (upper leaftlet having more and lower one less). has anyone ever encountered a paper with such a simulation. Is it possible? Thanks for any help __

[gmx-users] commanf for wrapping

hi i want to wrap my lipid in water... which centres the lipid in water. I know a command for this in amber (iwrap ). Is there a corresponding command in gromacs thanks for your help Pragya Chohan _ Post free property ads on

RE: [gmx-users] position restrain

the > freezegrps options for your .mdp file, but doing so will typically cause > problems if you are using pressure coupling. > > -Justin > > Quoting pragya chohan <[EMAIL PROTECTED]>: > > > > > hi > > I have a system of protein, popc,water and Cl ions.

[gmx-users] pressure coupling for bilayers

hi i want to rum a NPT ensemble on my bilayer+protein system. What is the best pcoupletype to use. I have seen some posts on gmx user group advising anisotriopic type with tau_p 5.0 ps cpmpressibility: 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0 Another suggestion is welcome. Thanks in advance Pragya _

[gmx-users] position restrain

hi I have a system of protein, popc,water and Cl ions. I want to position restrain protein and water as without position restrain water is going into the membrane . So I made a group of protein and water together using make_ndx and then genpr. When i ran grompp i got the following error:

RE: [gmx-users] mdrun error

hi i tried to run the simulation with single alamethicin molecule but i am getting the same error as i was getting earlier. Warning: 1-4 interaction between 164 and>> 169 at distance 3.430 which is larger than the 1-4 table size 1.000 nm. I used the command $ genbox -cp alamethicin.gro -cs po

[gmx-users] (no subject)

hi. Has anyone used inflategro provided on "http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis";. I am having problem in using it. When I enter my gro file no lipids are removed. Please reply. _ Call friends with PC-to-PC

RE: [gmx-users] mdrun error

; From: [EMAIL PROTECTED]> To: > gmx-users@gromacs.org> Subject: RE: [gmx-users] mdrun error> > Quoting pragya > chohan <[EMAIL PROTECTED]>:> > > Thanks Justin for your reply. I am > generating the starting structure through> > genbox.> > I adde

RE: [gmx-users] mdrun error

Thanks Justin for your reply. I am generating the starting structure through genbox. I added popc as solvent around alamethicin after aligning alamethicin in a box and centering it in the box and followed same procedure for popc also. Do you have any better way? > Date: Sat, 10 Nov 2007 10:22

RE: [gmx-users] mdrun error

ely, search the list for some of my posts from around a year ago - NVT> and minimization of a lipid bilayer (or search for my name, they should come up> as well). I suspect you have bad contacts in your starting structure.>> -Justin>> Quoting pragya chohan :>>>>&

[gmx-users] mdrun error

hi i am trying to run mdrun for protein in membrane system. When i run mdrun i get a warning Step -2, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 2.144082 (between atoms 12433 and 12434) rms 0.216090 bonds that rotated more than 30 degrees: atom 1 atom 2 angl

RE: [gmx-users] installation error

> Date: Thu, 8 Nov 2007 12:35:29 +1100> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] installation error>> pragya chohan wrote:>> hi>> I had installed make_hole utility earlier but when i t

[gmx-users] installation error

hi I had installed make_hole utility earlier but when i tried to run: make_hole.pl -f box_popc.pdb -o hole_popc.pdb -r 9.0 -lipat P8 -lipid POPC -cx 51.5 -cy 51.8 I get : bash: make_hole.pl: command not found. I tried reinstalling it by ./configure which completed successfully but when i ran mak

RE: [gmx-users] alamethicin error

> Date: Fri, 2 Nov 2007 09:39:36 +1100> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] alamethicin error>> pragya chohan wrote:>> i got this error "atom C not found in residue 84PHL while combin

RE: [gmx-users] gramicidin A

> Date: Sat, 3 Nov 2007 19:23:32 +1100> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] gramicidin A>> pragya chohan wrote:>> hi>> I was trying to run pdb2gmx command for gramicidin and noticed

[gmx-users] gramicidin A

hi I was trying to run pdb2gmx command for gramicidin and noticed it has some D-amino acids. Reading the earlier mail wjich states that: It's not too difficult to add a new residue to the topology database. Have a look in the file ff.rtp, where is the force field you are using. You can proba

[gmx-users] alamethicin error

i got this error "atom C not found in residue 84PHL while combining tdb and rtp" when i tried to do pdb2gmx the commamd used is: pdb2gmx -ter -ff gmx -f alamethicin.pdb -o alamethicin.gro -p ala.top Select N-terminus type (start) 0: NH3+ 1: NH2 2: None 2 N-terminus: None Select C-terminus type

[gmx-users] itp for alamethicin

hi... i have to make an itp file for alamethicin already tried prodrg2 but no success. pls suggest a way for making .itp file .. residue already defined in ffgmx.rtp. ...already read earlier query posted but could not find an ans. ___

[gmx-users] grompp error for alamethicin

hi ... when i run grompp i get an error " No such moleculetype Protein " ... i included itp for ACE and AIB after generating them from PRODRG2 server... my top file is : ; Include forcefield parameters #include "ffG43a1.itp" ; Include chain topologies #include "ace.itp" #include "aib.itp" ; I

[gmx-users] grompp error

hi... i have been trying to do grompp for the following file but am getting this error: There were 1 error(s) processing your inputWARNING 3 [file "popc.top", line 32]: 7380 non-matching atom names atom names from popc.top will be used atom names from popc.pdb will be ignored double-checking

[gmx-users] simulation popc

hi i m pragya, i found this article i used ffG43a1 and got this error when ran grompp: Atomtype 'CA' not found! . i m using popc128a.pdb from tieleman site and m using "lipid.itp" #include "ffG43a1.itp"#include "lipid.itp"#include "popc.itp" #ifdef FLEX_SPC#include "flexspc.itp"#else#incl