[gmx-users] Problem in downloading source code

t into the problem. Sincerely, B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search t

Re: [gmx-users] Problem in downloading source code

that I use for downloading, is Internet explorer of windowsXP. With thanks, B.Nataraj On Tue, 23 Oct 2007 16:21:44 +1000, "Mark Abraham" <[EMAIL PROTECTED]> said: > raja wrote: > > Dear sir, > > There is a problem in accessing your site for downloading gromacs sourc

Re: [gmx-users] Problem in downloading source code

## The try is going on and on Please suggest me any other alternative.. With thanks ! B.Nataraj On Tue, 23 Oct 2007 09:51:57 +0200, "Florian Haberl" <[EMAIL PROTECTED]> said: > Hi, > > > On Tuesday, 23. October 2007 09:24, raja wrote: >

[gmx-users] Source code through email

, B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - I mean, what is it about a decent email service? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] segmentation fault at middle of MD run

to restart this run from this stage. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo

[gmx-users] Value for bonded force constant (Kb)

Dear gmxions, Could any one give me the value for bonded force constant (Kb) to be used for restraining ,F(II) and ligating atoms of proteins ( 2 HISs and 1 ASP)using harmonic potential (type 6). With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm

[gmx-users] Value for bonded force constant (Kb)

correct me ): . With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Send your email first class ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't pos

Re: [gmx-users] Value for bonded force constant (Kb)

w the validity of my judgement. With Thanks ! B.Nataraj On Wed, 10 May 2006 13:50:17 +0200, "Tsjerk Wassenaar" <[EMAIL PROTECTED]> said: > Hi Raja, > > No objections from my side. But if you could also include the > references resulting from your literature study, that

Re: [gmx-users] Value for bonded force constant (Kb)

2006 05:16:26 -0700, "raja" <[EMAIL PROTECTED]> said: > Hi Mr Tsjerkw, > Thanks for your mail. Infact I intented to attach > the reference link but I missed it. Anyway here is the link where I > taken > the value of Kb. Infact the reference only talk between Fe and

[gmx-users] Shutting down in Windows2000

windowsXP. With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Accessible with your email software or over the web ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman

Re: [gmx-users] Shutting down in Windows2000

for final production phase of MD run. Can it be the cause? With thanks! B.Nataraj On Mon, 12 Jun 2006 16:24:14 +1000, "Mark Abraham" <[EMAIL PROTECTED]> said: > raja wrote: > > Dear Gmxions, > > While I run MD (Gromacs 3.3.1) in cygwin under windows2000

[gmx-users] Reg do_dssp in cygwin

thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - mmm... Fastmail... ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the

[gmx-users] analysing ndx file of g_hbond

is to know how many hbond listed in index file are belong to main chain atoms. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - The way an email service should be ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] analysing ndx file of g_hbond

t; <[EMAIL PROTECTED]> said: > On Wed, 2006-06-28 at 04:29 -0700, raja wrote: > > Dear all, > > > > The index file produced by g_hbond listing many rows of hbonds making > > atoms combination. Is there a way to get the corresponding residue and > > atom name for

[gmx-users] Analysing using InsighII Decipher

Dear All, Any strategy available for analyzing gromacs trajectory in insightII, Decipher module. Kindly let me know. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Choose from over 50 domains or use your own ___ gmx

[gmx-users] Hbond dynamic representation in MD movie

Hi all, Is there a tool known for displaying hbonds dynamically during gromacs trajectory visualization process and should also have facility to make MD movie out of it. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service

Re: [gmx-users] ZN HIS binding

HIS NE2 1 HEMEFE 1 0.2 HIS1HEME*HIS > NE2 1 ZIH ZN 1 0.25HISZZIH* > > > but it dont resolve my problem > > Thanks ! -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A fast, anti-spam email ser

[gmx-users] using DSSP outside gromacs

for with any of you? Looking for your suggestions... With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

[gmx-users] R.M.S.I.P. calcuation Reg..

Hi all, How to calculate the r.m.s.i.p.(Root mean square inner product) value (or matrix) between set of many eigen vectors file. Is it possible in groamcs in-build utilities ? Thanks in advance ! By, B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - And now for

[gmx-users] R.M.S.I.P for identical eigenvectors not equal to 1 ?

regarding this issue? With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A fast, anti-spam email service. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't

Re: [gmx-users] R.M.S.I.P for identical eigenvectors not equal to 1 ?

, "Tsjerk Wassenaar" <[EMAIL PROTECTED]> said: > Hi Raja, > > Did you use the same eigenvectors from the same simulation over the > same stretch of time? For two (parts of a) simulation(s) of the same > system, the RMSIP value will only converge to one in the limit

Re: [gmx-users] R.M.S.I.P for identical eigenvectors not equal to 1 ?

" $N1 \n "; } close(F2) } print "The Value of N1 is $N1 \n"; $N1 = $N1/10; $N1 = sqrt ($N1); print "$N1"; close(F1) ; #---End of code--- With thanks ! B.Nataraj On Fri, 28 Jul

Re: [gmx-users] R.M.S.I.P for identical eigenvectors not equal to 1 ?

Hi Tsjerk, Oops, I am sorry and thanks for your help and providing me the program. With thanks! B.Nataraj On Fri, 28 Jul 2006 13:35:48 +0200, "Tsjerk Wassenaar" <[EMAIL PROTECTED]> said: > Hi Raja, > > Okay, you're not using the eigenvectors, you're using th

[gmx-users] R.M.S.I.P. between two halves of same simulation

. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Does exactly what it says on the tin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't pos

[gmx-users] Fe(II) at active site

s flipped and Asp as a single residue held the Fe (II) at its original position. So now please tell me whether this simulation is valid? More all-globular validation of the entire simulation is perfect. Kindly give me yours valid opinion. With thanks! B.Nataraj -- raja [EMAIL

Re: [gmx-users] Fe(II) at active site

> 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/user

Re: [gmx-users] Fe(II) at active site

Hi XAvier, Well, you made a point of "Ions are big issue in MD simulations". Could you please hint me what possible issues, so I can search relavent to those keywords. With thanks ! B.Nataraj On Sat, 29 Jul 2006 14:45:14 +0200, "X.Periole" <[EMAIL PROTECTED]> said: &g

[gmx-users] g_hbond account dieletric medium ?

, how I can prove that hydrogen bonds formed between those groups are by overcoming the dielectric medium of waters? With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A fast, anti-spam email service. ___ gmx-users mailing

Re: [gmx-users] g_hbond account dieletric medium ?

list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - The way an email service should be ___ gmx-users mailing

Re: [gmx-users] g_hbond account dieletric medium ?

can prove that proton is shared between those atoms. Sorry if I am making any mistake at fundamental level. With thanks! B.Nataraj On Thu, 03 Aug 2006 16:12:41 +0200, "David van der Spoel" <[EMAIL PROTECTED]> said: > raja wrote: > > Hi XAvier, > > Thanks again, I

Re: [gmx-users] g_hbond account dieletric medium ?

by reading a book or journal. Regards, B.Nataraj in On Thu, 03 Aug 2006 17:29:19 +0200, "David van der Spoel" <[EMAIL PROTECTED]> said: > raja wrote: > > Thanks spoel, > > The g_hbond merely report formation of hydrogen bonds because of two > > electronegative a

[gmx-users] channel size calculation between active site lid

the average opening size (Pore or channel size) during simulation through which the substrate believed to reach the active site. How to do it either within or outside of gromacs? With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Accessible with your email software

[gmx-users] Ploting xvg file in R statistic package

Hi all, Anyone know , to convert xvg formated data of gromacs for analysis in R statistical package. with thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ gmx-users mailing list

[gmx-users] How to treat CSD residue in protein

-- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ 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

[gmx-users] How to use deprotonated Cys

a lot of mails regarding this issue most of them are in “2004 archives”. Hope things are now changed and I can get some direct solution for this from any of you. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Same, same, but different

Re: [gmx-users] How to use deprotonated Cys

Zn along with other two partners,( 2 His NE2 atoms). Now please tell me how to treat this Cys in opls force field. With thanks! B.Nataraj On Thu, 24 Aug 2006 17:21:22 +0200, "David van der Spoel" <[EMAIL PROTECTED]> said: > raja wrote: > > Hi all, > > I have pr

Re: [gmx-users] How to use deprotonated Cys

! B.Nataraj On Fri, 25 Aug 2006 06:24:58 +0200, "David van der Spoel" <[EMAIL PROTECTED]> said: > raja wrote: > > Dear david, > > Thanks for your reply. There are two forms exist for the protein of my > > interest and one is native form and other is with lig

Re: [gmx-users] How to use deprotonated Cys

Dear David, Thanks for your support as you are always. Regards, B.Nataraj On Fri, 25 Aug 2006 06:46:19 +0200, "David van der Spoel" <[EMAIL PROTECTED]> said: > raja wrote: > > Dear David, > > Thanks again, yes Cys is having fourth ligand as water to complete the &

[gmx-users] Req for computer config for windows to run gromacs

. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Send your email first class ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe reques

Re: [gmx-users] Req for computer config for windows to run gromacs

Dear David, Thanks, but Linux is not possible because of other users not aware of that OS. Well, can you make details for some best hardware configuration. With thanks! B.Nataraj On Tue, 29 Aug 2006 08:41:20 +0200, "David van der Spoel" <[EMAIL PROTECTED]> said: > raja

Re: [gmx-users] Req for computer config for windows to run gromacs

Thanks Mark for your suggestions. On Tue, 29 Aug 2006 18:46:30 +1000, "Mark Abraham" <[EMAIL PROTECTED]> said: > raja wrote: > > Dear David, > > Thanks, but Linux is not possible because of other users not aware of > > that OS. Well, can you make details for

Re: 回复： Re: [gmx-users] r.m.s.i.p

7;t post? Read http://www.gromacs.org/mailing_lists/users.php > > > > - > > 雅虎免费邮箱-3.5G容量，20M附件 -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - I mean, what is it about a decent email service? ___

[gmx-users] Simulation single unit of a dimer

performing the same catalytic activity but act individually. Your thought for this question would be very useful for me. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - IMAP accessible web-mail ___ gmx-users mailing

Re: [gmx-users] Simulation single unit of a dimer

Dear David, Thanks for your reply and your suggestion is helping me. By, B.Nataraj On Mon, 06 Nov 2006 09:12:32 +0100, "David van der Spoel" <[EMAIL PROTECTED]> said: > raja wrote: > > Dear gmxions, > > The protein, which I am going to simulate, is a dimer, but

[gmx-users] RESP fitting using MOPAC

! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Access all of your messages and folders wherever you are ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] RESP fitting using MOPAC

harges - which means > that RESP would be the method of choice for AMBER but not necessarily > for different FFs. > > You have free software that you can use for such calculations such as > GAMESS-US and NW-CHEM (though you need to obtain a licence to use them). > > Ran. >

[gmx-users] Including water in for restraining

108 Fatal error: [ file "Protein_ion_A.itp", line 5847 ]: Atom index (2905) in bonds out of bounds (1-2900) --- How to restraint molecule which is present in out of this itp file ? With thanks ! B.Nataraj -- raj

Re: [gmx-users] Including water in for restraining

your protein... remove any lines that reference water > or zinc. > > If you need further help, please specify exactly what you have done so > far, where you got your files, and what the files look like. > > Chris. > > > > ______

[gmx-users] Retaining water in protein chain

Dear gmxions, I want to retain one of water molecule in main chain of protein while converting it into separate chains as it is usualy done after genion using pdb2gmx. How can I do it ? With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Access all of your

[gmx-users] water in protein itp file

topic, but not received any replies, are http://www.gromacs.org/pipermail/gmx-users/2006-November/024680.html http://www.gromacs.org/pipermail/gmx-users/2006-November/024682.html http://www.gromacs.org/pipermail/gmx-users/2006-November/024696.html With thanks! B.Nataraj -- raja [EMAIL

Re: [gmx-users] water in protein itp file

2006 14:49:27 +1100, "Mark Abraham" <[EMAIL PROTECTED]> said: > raja wrote: > > Dear gmxions, > > I want to include one crystal water within protein itp, to further > > restrict it by harmonic bond with metal ion at the active site. > > In other words, on

Re: [gmx-users] water in protein itp file

water molecule. With thanks! B.Nataraj On Tue, 14 Nov 2006 15:22:30 +1100, "Mark Abraham" <[EMAIL PROTECTED]> said: > raja wrote: > > Dear Mark, > > Thanks for your immediate reply and good solution. But until before > > yours this mail, I was thinking th

Re: [gmx-users] water in protein itp file

Dear Mark, Thaks for your replies and I end this discussion with this. B.Nataraj On Wed, 15 Nov 2006 11:51:37 +1100, "Mark Abraham" <[EMAIL PROTECTED]> said: > raja wrote: > > Dear Mark, > > Well and thanks again, QM-MM is a good option, as you said for analy

Re: [gmx-users] Including water in for restraining

; > It is unclear to me if the [ exclusions ] section is necessary or even > advisable. > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don'

Re: [gmx-users] ElecStatic for two residues and mdrun rerun issues

fied by my this run, if you can confirm me the introduction or alteration of those parameters is meant for only speedup purpose and not for anything else B.Nataraj On Wed, 22 Nov 2006 08:57:57 +1100, "Mark Abraham" <[EMAIL PROTECTED]> said: > raja wrote: > > Hi g

Re: [gmx-users] ElecStatic for two residues and mdrun rerun issues

Dear Mark, Thanks for your untiring efforts to reply back to all. Regards, B.Nataraj On Wed, 22 Nov 2006 16:41:40 +1100, "Mark Abraham" <[EMAIL PROTECTED]> said: > raja wrote: > > Thanks Mark for your reply. So the “parameters nstlist=0”, > > “unconstrained_sta

Re: [gmx-users] ElecStatic for two residues and mdrun rerun issues

Dear Mark, Thanks for your untiring efforts to reply back to all. Regards, B.Nataraj On Wed, 22 Nov 2006 16:41:40 +1100, "Mark Abraham" <[EMAIL PROTECTED]> said: > raja wrote: > > Thanks Mark for your reply. So the “parameters nstlist=0”, > > “unconstrained_sta

[gmx-users] Script for atom typing for AMBER convention

force field downloaded from ffAMBER site. By Thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - I mean, what is it about a decent email service? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman

Re: [gmx-users] (no subject)

for propanol compound > and generate a suitable topology in water solvent. > > thanks a lot > > > > > Thank a lot foryour guidance. > > > > - > Want to start your own business? Learn how on Ya

[gmx-users] Script for coverting ITP and gro file to Autodock pdbqs

mated one. With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - mmm... Fastmail... ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscrib

[gmx-users] Partial charge distribution for metal ligating atoms

ng default partial charge of SG-Cys from -0.8844 to -0.6944, Should I adjust its net formal charge to -1 or to 0? Then on what basis I can adjust rest of the atoms’ partial charges. Kindly reply me. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Does exactly wh

Re: [gmx-users] Partial charge distribution for metal ligating atoms

Tue, 28 Nov 2006 17:51:04 +1100, "Mark Abraham" <[EMAIL PROTECTED]> said: > raja wrote: > > Hi gmxions, > > There are many references, say that Zn2+ partial charge should be > > reduced to ~0.7 rather than the force field default value of 2. In line > > wi

Re: [gmx-users] Partial charge distribution for metal ligating atoms

ette[at]mpi-bpc.mpg.de > mgoette2[at]gwdg.de > WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ > > > raja wrote: > > Dear Mark, > > Thanks for your reply. Well, I have well taken your point of making > > separate charge group constituting Zn and its residue

Re: [gmx-users] Partial charge distribution for metal ligating atoms

Thanks Mark for your valuable suggestions and dedicating your valuable time for me. On Wed, 29 Nov 2006 00:47:33 +1100, "Mark Abraham" <[EMAIL PROTECTED]> said: > raja wrote: > > Thanks Goette for your mail. So system neutrality is restored as per > > your adv

[gmx-users] Inner product for two proteins eignevector trajectory

of different residue length, How to overcome this issue? Kindly reply me. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Access all of your messages and folders wherever you are ___ gmx-users

Re: [gmx-users] Inner product for two proteins eignevector trajectory

sjerk Wassenaar" <[EMAIL PROTECTED]> said: > Hi Raja, > > Do the covariance analysis on a subset of your atoms, which is equal > in both structures, using index files. > > Cheers, > > Tsjerk > > On 11/29/06, raja <[EMAIL PROTECTED]> wrote: > &g

Re: [gmx-users] Inner product for two proteins eignevector trajectory

Hi Tsjerk, Thanks for your mails and for sharing valuable insight in current discussion topic. B.Nataraj On Wed, 29 Nov 2006 14:28:17 +0100, "Tsjerk Wassenaar" <[EMAIL PROTECTED]> said: > Hi Raja, > > Now the only reason that I did (briefly) read the paper you

Re: [gmx-users] Script for coverting ITP and gro file to Autodock pdbqs

net formal charge and zero is not mandatory. Please reply me. B.Nataraj On Wed, 29 Nov 2006 19:16:52 +0330, "Mahnam" <[EMAIL PROTECTED]> said: > In God We Trust > Hello Dear raja > I think that the charges in itp of Gromacs don't match with charges in > Au

[gmx-users] AMBER atom type for Hydroxamate moeity

; N2 sp2 N in amino groups amber99_3914.01000 ; N3 sp3 N for charged amino groups (Lys, etc) amber99_4014.01000 ; N* sp2 N With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - The professional email service

Re: [gmx-users] AMBER atom type for Hydroxamate moeity

Thanks Mark for your reply. And sorry about missing one hydrogen in my drawn topology... B.Nataraj On Thu, 30 Nov 2006 23:12:10 +1100, "Mark Abraham" <[EMAIL PROTECTED]> said: > raja wrote: > > Dear gmxions, > > I am writing a topology for a ligand using AMB

Re: [gmx-users] AMBER atom type for Hydroxamate moeity

via QM, > e.g. with Gaussian...Further parameters, like force-constants and > dihedrals could also be evaluated... > > But what's against an expensive random number generator? > I fear I'm doing this with FEP all day long...;) > > Raja: We are (mostly) not doing

Re: [gmx-users] AMBER atom type for Hydroxamate moeity

Hi Florian, Thanks for your mail and introducing me the Antechamber site. I am trying out there in that site. B.Nataraj On Thu, 30 Nov 2006 16:00:39 +0100, "Florian Haberl" <[EMAIL PROTECTED]> said: > hi, > > On Thursday 30 November 2006 13:01, raja wrote: > > D

Re: [gmx-users] AMBER atom type for Hydroxamate moeity

> > cheers, > nr > > > On 11/30/06 7:00 AM, "Florian Haberl" > <[EMAIL PROTECTED]> wrote: > > > hi, > > > > > > > > On Thursday 30 November 2006 13:01, raja wrote: > > > >> Dear gmxions, > > > >&

Re: [gmx-users] AMBER atom type for Hydroxamate moeity

Hi Mark, Thanks again, But I am Indian...will either of those flavour work for me :-) B.Nataraj On Fri, 01 Dec 2006 16:21:59 +1100, "Mark Abraham" <[EMAIL PROTECTED]> said: > raja wrote: > > Hi Goette, > > Thanks for your mail. I have just find an article done a

Re: Re: [gmx-users] Error while compilation of Gromacs3.3.1.....in SGI Octane

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://

[gmx-users] RNA gro to pdbqs

tried to use ADT tool as I use it for protein , but It fails to recognize the new residue types of AMBER99 specific (ie., RA5,RA3, RC...etc.,) . Experienced out there help me to fix this problem. With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Faster than the

Re: [gmx-users] ligand in vacuum trajectories (PRODRG)

pology... > Generated 1284 of the 1485 non-bonded parameter combinations > processing coordinates... > Fatal error: number of coordinates in coordinate file (drg.gro, 25) > does not match topology (drg.top, 0) > > > Regards > > Dariusz -- raja [EMAIL PROTECTED

[gmx-users] How to make drug for OPLSA ff compatiable

itp file. Any straight forward solution for this ? With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - The way an email service should be ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/lis

Re: [gmx-users] How to make drug for OPLSA ff compatiable

mp; computational biophysics department > Am Fassberg 11 > 37077 Goettingen > Germany > Tel. : ++49 551 201 2310 > Fax : ++49 551 201 2302 > Email : mgoette[at]mpi-bpc.mpg.de > mgoette2[at]gwdg.de > WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ > > &g

[gmx-users] Drug-Enzyme simulation

is very much needed ! With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Faster than the air-speed velocity of an unladen european swallow ___ gmx-users mailing listgmx-users@gromacs.org ht

[gmx-users] Error : Molecule type redefined

of mismatch coordinate between protein.top and protein.gro file as expected. What is the solution ? With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - mmm... Fastmail... ___ gmx-users mailing listgmx-users

[gmx-users] Computing RMSD for RNA structure

! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Send your email first class ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests t

[gmx-users] Solvent accessbility of ligand in RNA

indirectly. If not within GROMACS , kindly give me the direction to do the same in any of publicaly avilable software. With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - The way an email service should be ___ gmx-users

[gmx-users] Ligand moves out of box during EM steps

consideration in energy minimization? and how to prevent my ligand from moving it from its initial position. With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Or how I learned to stop worrying and love email again

[gmx-users] Ligand moves out of box during EM steps

active site and located itself at the corner of the water box. Kindly provide me the solution to retain the ligand at its original position during minimization step! With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Email service worth paying for. Try

Re: [gmx-users] Ligand moves out of box during EM steps

AIL PROTECTED]> said: > Hi Raja, > > Probably PBC. Nothing wrong, just visual. You can try to center your > system > on the ligand before starting the simulation, which should keep it "in > place". > > Tsjerk > > On 3/22/06, raja <[EMAIL PROTECTED]&g

Re: [gmx-users] Ligand moves out of box during EM steps

ith thanks ! B.Nataraj On Wed, 22 Mar 2006 14:31:42 +0100, "Tsjerk Wassenaar" <[EMAIL PROTECTED]> said: > Hi Raja, > > When you generate a .tpr file (for whatever purpose) all molecules will > be > mapped to a rectangular box as good as possible. For this, the first at

[gmx-users] Req for script to make rtp entro of ligand with ffoplsa compatiable

Dear GMXIONS, Kindly provide me a script to make rtp entry for a ligand to use it for oplsa force field file. With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Access your email from home and the web

Re: [gmx-users] Ligand moves out of box during EM steps

original > > complex and fit it to the minimized protein (using DeepView or any other > > program like Whatif, for example), then save only the ligand of the > > complex and use these new coordinates to feed the gro file of the > > minimized protein. > > Hope I unders

Re: [gmx-users] Ligand moves out of box during EM steps

.conf" but where comes the file protein.conf in previous step. With thanks ! B.Nataraj On Thu, 23 Mar 2006 09:45:46 +0100, "Tsjerk Wassenaar" <[EMAIL PROTECTED]> said: > Raja, > > Try: > > pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh

Re: [gmx-users] Ligand moves out of box during EM steps

, "Tsjerk Wassenaar" <[EMAIL PROTECTED]> said: > Hi Raja, > > The "protein.conf" I took from your mail.., so that is whatever you did > to > get "protein.conf"! I think in your mail that was the structure obtained > from pdb2gmx combined with the lig

[gmx-users] Error: relative constraint deviation after LINCS

) ### With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - The way an email service should be ___ gmx-users mailing listgmx

[gmx-users] Error: relative constraint deviation after LINCS

) ### -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - The way an email service should be ___ gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Error: relative constraint deviation after LINCS

lar problem as you did when I had set pme_order to 6, and I > don't know why... > > --Tom > > On Mar 28, 2006, at 10:28 PM, raja wrote: > > > Hi gmxs, > > No reply yet for this posting, so I reposting the same > > error...Please give me the di

Re: [gmx-users] Error: relative constraint deviation after LINCS

der to 6, and I > > > don't know why... > > it's a known bug, please fetch the new pme.c from the ftp site. > > > > > > --Tom > > > > > > On Mar 28, 2006, at 10:28 PM, raja wrote: > > > > > >> Hi gmx

Re: [gmx-users] Error: relative constraint deviation after LINCS

t; <[EMAIL PROTECTED]> said: > Sorry, but the right way to do it is to recompile GROMACS. Annoying, > yes, but necessary :) > > --Tom > > On Mar 30, 2006, at 1:55 AM, raja wrote: > > > Dear all, > > Thanks for your thoughts and suggestions. Please tell

Re: [gmx-users] Error: relative constraint deviation after LINCS

Dear Mr.Mark Abraham, Thanks for pointing out the way to retrive the old flags used. With thanks ! B.Nataraj On Thu, 30 Mar 2006 20:31:16 +1100, "Mark Abraham" <[EMAIL PROTECTED]> said: > raja wrote: > > Dear Tom, > >Its is really annoying, I rea

[gmx-users] configure problem in SGI

to a location in your home directory and provide the correct paths in .. ### With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Same, same, but different… ___ g

Re: [gmx-users] configure problem in SGI

fect. May I have to add these environmental variables in my .cshrc file ?. Please suggest me any other flags to be enabled or disabled to make configure to get path of fftw library files. With thanks! B.Nataraj On Mon, 03 Apr 2006 09:06:22 +0200, "David van der Spoel" <[EMA

Re: [gmx-users] configure problem in SGI

tallation instructions at > > http://www.gromacs.org/installation/index.php > > Based in the limited output below it looks as if you are either > trying to install an earlier version of Gromacs without support for > FFTW-3, or you have manually selected FFTW-2. > > Cheers

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