Re: [gmx-users] Lie method for binding free energy calculations

Hi, You can email me we have a tool for mmpbsa with gromacs Andrea Messaggio inviato dal mio ASUS MeMO Pad Justin Lemkul ha scritto: On 10/25/13 11:43 AM, Sajad Ahrari wrote: > is AMBER facilities the only way of approaching MM-PBSA calculations? could > you > lead me to any other software m

Re: [gmx-users] nstcalclr bug?

; Velocity generation is off > > gen-seed= 128742 > > ; number of steps for center of mass motion removal > > nstcomm = 1000 > > > > the mdout.mdp file says nstcalclr = 10, but gmxdump of the tpr file says > > nstcalclr = 0. If

[gmx-users] nstcalclr bug?

t I couldn't find the reason of this behaviour. is this a bug or am I doing wrong somewhere?? thanks for any helps and Andrea Spitaleri PhD D3 - Drug Discovery & Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 -- gmx-users mailing list

Re: [gmx-users] OPLS-AA parameters for Phospho-threonine and serine

Hi, Have look here: http://haddock.science.uu.nl/services/HADDOCK/library.html The ff used by HADDOCK is oplsx derived from opls. Maybe you can exploit them as starting point. Hope it helps And "Martin, Erik W" ha scritto: I've searched the literature and internet and can't seem to find an

Re: [gmx-users] different checkpoint from remd after crash

have a full set of matching .cpt files, but not with consistent names. Use gmxcheck to see the times. Mark On Fri, Apr 19, 2013 at 3:24 PM, andrea spitaleri wrote: Hi there, I am performing a remd (8 replica) using gromacs-4.5.3 Unfortunately, the job crashed for a problem with our cluster

[gmx-users] different checkpoint from remd after crash

-- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Fondazione Centro San Raffaele Centro di Genomica Traslazione e Bioinformatica Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site

Re: [gmx-users] MM-GB/SA analysis in Gromacs

Many thanks in advance and best regards Anna -- --------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Fondazione Centro San Raffaele Centro di Genomica Traslazione e Bioinformatica Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olg

Re: [gmx-users] force field parametrs for Mn2+

contains force field parameters for Mn 2+ . Thanks -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039

Re: [gmx-users] PLUMED plugin in gromacs for protein system

-- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site

[gmx-users] pdb2gmx -ter with cyclic peptide

r any help and -- ----- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-02264

Re: [gmx-users] angle between two domains connected at a hinge

Copenhagen -- ----- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://www.linke

Re: [gmx-users] gnuplot

ch Schloar, Prin. K. M. Kundnani College of Pharmacy, Colaba, Mumbai-05. Cont. No. +91 9769051866 -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano I

Re: [gmx-users] xvg plotting

ocess? Thank you in advance N.V. -- ----- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://ww

Re: [gmx-users] Error during PUMED installation for GROMACS-4.5.3

`./src/kernel//.deps/restraint_waterbridge.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_zpath.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/testderivatives.Po': No such file or directory touch: cannot touch `./src/k

Re: [gmx-users] xtc corrupted during REMD

tc options. Are all you xtc corrupted or only some? Are those which are corrupted all corrupted on the same frame or different ones? Roland -------- Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and

[gmx-users] xpm2ps tick display

-fontsize = 16 y-font = Times-Roman y-tickfontsize = 10 y-tickfont = Helvetica Any help_?? thanks in advance andrea -- ------- Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStati

Re: [gmx-users] copper cluster bond to histidines

mulations like these (exotic species)... But you had already > considered that. > > Hope this helps, > > Tsjerk > > On Wed, Aug 12, 2009 at 12:40 PM, andrea > spitaleri wrote: >> Dear all, >> I am going to run some MD simulation of a protein bearing a

[gmx-users] copper cluster bond to histidines

le inside of the Cu2+ cluster in a second study. Any suggestion, comments and anything else are very welcome. Thanks in advance Regards andrea -- ------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58

Re: [gmx-users] continuing a MD simulation on different architectures

he simulation step on my cluster (intel) using the previous >> cpt file and generating >> the new tpr on my cluster. I did it and it runs, however I was wondering >> about the physical and >> chemical reliability. >> >> thanks in advance >> >> Regard

[gmx-users] continuing a MD simulation on different architectures

generating the new tpr on my cluster. I did it and it runs, however I was wondering about the physical and chemical reliability. thanks in advance Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR

Re: [gmx-users] Converting 2-d molecule to 3-D

cs.org/mailing_lists/users.php -- ------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226434348/5622/3497/4922

[gmx-users] 4.0_beta1: 1 particles communicated to PME node 9 are more than a cell length out of the domain decomposition cell of their charge group

Hi again, in addition to the previous post, 4.0_beta1 crashes using 27 cpus and option -dd 3 3 3, whereas it goes fine using 24 cpus and not -dd option. any clue? Regards, andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific

[gmx-users] 4.0_beta1: 1 particles communicated to PME node 9 are more than a cell length out of the domain decomposition cell of their charge group

-dd 4 4 4 option). I hope this help in gmx debugging Regards, andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039

Re: [gmx-users] how to edit pdb file

bscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Ins

[gmx-users] benchmark: buying a new cluster

, Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153

Re: [gmx-users] Mn parameters

Hi all, sorry for the previous wrong links (Thanks to Mark): http://www.gromacs.org/pipermail/gmx-users/2002-April/001333.html http://www.gromacs.org/pipermail/gmx-users/2002-March/001000.html http://www.gromacs.org/pipermail/gmx-users/2006-July/022999.html Regards, andrea andrea spitaleri

[gmx-users] Mn parameters

or this FF. Previous post are: http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ and http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ Thanks in advance Regards andrea -- ------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT

Re: [gmx-users] g_mindist -pi option

! >> 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/users.php >> > > ___ > gmx-users

Re: [gmx-users] g_mindist -pi option

ailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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/m

Re: [gmx-users] g_mindist -pi option

nm. Any clue? thanks again Regards andrea andrea spitaleri wrote: > Hi there, > I have a complex protein-peptide in a box 6.5 6.5 6.5 with a starting > periodic image of 3.0 nm, > using PME and rlist=rvdw=rcoulomb=0.9. > Now, I use to check the pi dist during my simulation in ord

[gmx-users] g_mindist -pi option

nts? is it true this value or is it pbc artefact? Thanks in advance Regards, and ps. gmx3-3-1 compiled on suse-10.2 gcc-v 4.1.2 -- ------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (I

Re: [gmx-users] Prot_prep_problem

I apology for the incorrect spelling of your name ... I have an automatic reply format which sometimes does weird stuff ... Sorry Prasenjit, really. Regards andrea andrea spitaleri wrote: > HI Pkmukher, > I use to use opls for nmr structures in order to keep the all-hydrogen in the >

Re: [gmx-users] Prot_prep_problem

g 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 the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can&#

Re: [gmx-users] splitting of chains

rface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT S

Re: [gmx-users] genion halted

Hi yes I do use genion and g_rdf properly with 4.0.2 Regards and Sampo Karkola wrote: > Hi, > > so you got genion working with 4.0.2? > > Sampo > > andrea spitaleri wrote: >> gcc-4.0.2 seems ok for gmx-3.3.1 >> I have also submitted in bugzilla a similar pr

Re: [gmx-users] genion halted

gcc-4.0.2 seems ok for gmx-3.3.1 I have also submitted in bugzilla a similar problem with g_rdf Regards andrea Sampo Karkola wrote: > Hi, > > the same one, gcc-4.1. Have you tried with other versions? > > Sampo > > andrea spitaleri wrote: >> Hi >> whic

Re: [gmx-users] genion halted

requests to the list. Use the www > interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Ita

[gmx-users] ion contact: rdf does not tend to 1

-homogeneous situation?. In few words, after few nm there are not oxygen atoms interacting with the ion. Thanks Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano

Re: [gmx-users] rdf bug in 3.3.1 depending on the gcc?

Hi, okay I will submit the bugzilla. Thanks Regards, andrea David van der Spoel wrote: > andrea spitaleri wrote: >> Hi all, >> I have suspicious that g_rdf is bugged or at least it has a problem >> depending on the machine type. >> In one pc works and in another it han

[gmx-users] rdf bug in 3.3.1 depending on the gcc?

115 (prerelease) (SUSE Linux) Suse 10.2 2.6.18.2-34-default I did not find any entry in the bugzilla. Thanks Regards, Andrea -- ------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina

Re: [gmx-users] mindist during MD

>> thanks in advance >> an't post? Read http://www.gromacs.org/mailing_lists/users.php > > what mindist? > what cutoff? PME or not? > -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR,

[gmx-users] PCoorA and Energies

advance Regards, andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom

Re: [gmx-users] peptide coming out of the box

/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/users.php > > _______

Re: [gmx-users] coordination number of ion: rdf integration

efficient volume should be 10x10x10? I cannot figure out how did you retrieve this conclusion. Thanks for your help anyway, Regards Andrea -- ------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina

Re: [gmx-users] gmxcheck and trjconv

Hi, however in md0.log the right time is reported (69 and not 70) and David van der Spoel wrote: > andrea spitaleri wrote: >> Hi all, >> silly question. I have checked a trr with gmxcheck and I get this >> output below: >> Item#frames Timestep (ps) >>

Re: [gmx-users] gmxcheck and trjconv

... gmx version 3.3.1 Regards andrea David van der Spoel wrote: > andrea spitaleri wrote: >> Hi all, >> silly question. I have checked a trr with gmxcheck and I get this >> output below: >> Item#frames Timestep (ps) >> Step701 >> Time

[gmx-users] gmxcheck and trjconv

ndrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- ___ gmx-users mailing

Re: [gmx-users] explicit hydrogen-bond

nd it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Mil

[gmx-users] explicit hydrogen-bond

thanks andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom

[gmx-users] problem running posre

me input a simulation with "no" position restraints the runs goes fine. I tried using posrefc 1000 and lower (200). Same result. Any suggestion? Regards andrea -- ------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomo

[gmx-users] remd and nmr

hinking to feed into gromacs one of this structure (the best in procheck_nmr) and to see whether the REMD simulation might explore also the other configurations found by cns and give much more clue on the relative stabilty. Any suggestion? thanks in advance andrea -- ---

Re: [gmx-users] additional peptide bond: cyclic peptides

e or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biom

Re: [gmx-users] cyclic peptides

EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnm

Re: [gmx-users] Recover corrupted files from DVD

interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ------- Andrea Spitaleri Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Ita

[gmx-users] octahedron and trr

trjconv) and onto it the trr file. Thanks in advance Regards Andrea -- --- Andrea Spitaleri Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom

Re: [gmx-users] does gromos force field can explain pi-pi interaction

Interactions Chemistry - A European Journal Volume 8, Issue 13 , Pages 2860 - 2867 Gianni Chessari, Dr. 1, Christopher A. Hunter, Prof. 1 *, Caroline M. R. Low, Dr. 2, Martin J. Packer, Dr. 1, Jeremy G. Vinter, Dr. 2, Cristiano Zonta Regards andrea -- --- Andrea

[gmx-users] parameters for Mn2+

even suggestions for dealing with Mn2+?? Thanks in advance Andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom

Re: [gmx-users] Arbitrary S-S bonds

post? Read http://www.gromacs.org/mailing_lists/users.php -- ------- Andrea Spitaleri Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnm