[gmx-users] Re: Re: calculating dihedral properties

Dear Justin, sorry for the late answer and acknowledgements... Please see below my comments. Anna __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Giovanni Paolo II, 132 84084 Fisciano (SA

[gmx-users] calculating dihedral properties

-- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Giovanni Paolo II, 132 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 Web page: http://www.unisa.it/docenti/annamarabotti/index

[gmx-users] how to deal with LINCS warnings despite prolonged stabilization of the system?

with the simulations that went well. I don't see any significant difference (if somebody wants to see, I can provide the files) Thanks a lot Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Giovanni

Re: Re: [gmx-users] how to deal with LINCS warnings despite prolonged stabilization of the system?

of the protein ligand influence not only the ligand itself but also the protein determining the starting of LINCS WARNINGS on atoms that apparently are (relatively) far from the ligand? Thanks a lot Anna __ Anna Marabotti, Ph.D. Assistant Professor Department

[gmx-users] still dealing with GFP-like chromophore with LINCS warnings

to Parrinello? What do you suggest me to do? Thanks a lot Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Giovanni Paolo II, 132 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39

[gmx-users] Re: Re: Re: help with a chromophore of GFP

that all is clear; always many thanks for your help, and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax

[gmx-users] Re: Re: Re: Re: help with a chromophore of GFP

__ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 When a man with a gun meets a man with a pen, the man

[gmx-users] Re: Re: Re: Re: help with chromophore of a GFP

know how to find a way to send you all information. Thanks Anna __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089

[gmx-users] Re: help with chromophore of a GFP

Dear gmx-users, dear Mark, thank you for all the help you are giving me for this subject. I'm still proceeding to my target.. Thanks to your previous suggestions, I was able to parametrize bonds and angles of CFY. Now I'm dealing with dihedrals... In the parameter files derived by Antechamber

[gmx-users] Re: Re: help with chromophore of a GFP

Dear gmx-users, I'm still dealing with my problem of obtaining parameters for my chromophore of the GFP family, in order to treat it as a new residue. I'm trying (VERY hardly) to add missing parameters into ffbonded.itp file for AMBER99SB ff, using those parameters found in files calculated

[gmx-users] Re: Re: help with chromophore of a GFP

the data I have? I don't recognize at all the value... I know that this is not strictly referred to Gromacs, anyway could you please tell me at least how can I find information on how to add these parameters properly? Anna __ Anna Marabotti, Ph.D

Re: [gmx-users] help with chromophore of a GFP

suggestions on how to treat hydrogens that are bound to a residue which is so different from classic standard residues. Has anyone made this before (I am sure yes)? Could you please give some suggestions? Thank you very much Anna __ Anna Marabotti

Re: [gmx-users] help with chromophore of a GFP

, Anna MARABOTTI amarabo...@unisa.it [5] wrote: I decided to use Amber99SB since it seemed the better for my scope, then I start trying to parameterize it. This is what I did: * I used Pymol to add H to my pdb file, since I want to use an all H forcefield and since Antechamber (see below) does

[gmx-users] help with chromophore of a GFP

Dear gmx-users, it's about two weeks that I'm trying to solve this problem, and I can't, so I'm asking your help. I want to do some MD simulations on a protein of the family of green fluorescent protein. This protein, as you know, has a chromophore (CFY) derived from four residues of the

[gmx-users] problem with a complex cofactor

-- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 When a man with a gun meets a man with a pen, the man

[gmx-users] Re: Re: problem with a complex cofactor

Thank you Justin for your suggestion. I searched into the archive to find something about GFP chromophore before writing to the list, but I did not find anything, I' d try to search better. Anna __ Anna Marabotti, Ph.D. Assistant Professor Department

[gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric), and topologies to Amber format

the trajectory is not in the classic cubic format. This is just for records since it is a recurrent query in the gmx-user archive, still apparently with no solution. Many thanks in any case and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant

[gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format

for your kind answer and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo

[gmx-users] how to convert a dodecahedric trajectory into a triclinic one?

, but I have some trouble in doing it, I don't understand which are the correct flags to use. Could anybody give me some suggestion about this problem? Many thanks in advance and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant Professor

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

program? Many thanks in advance and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E

[gmx-users] PBC treatment: need an explanation

the spikes related to jump across the periodic boundaries? Thank you very much for help, and best regards Anna Anna Marabotti, Ph.D. Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man

[gmx-users] quick question about restart

Anna Marabotti, Ph.D. Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with a gun is a dead man (Roberto Benigni, about Roberto Saviano) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

[gmx-users] R: Re: several questions about g_hbond -contact

, 21 Feb 2012 15:39:48 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] several questions about g_hbond -contact To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4f440114.9010...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna

[gmx-users] several questions about g_hbond -contact

radius of 0.5 nm? Thanks in advance for your suggestions, and best regards Anna __ Anna Marabotti, Ph.D. Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with the gun

[gmx-users] a doubt about pbc nojump or mol or whole

would be very appreciated. Many thanks in advance and best regards Anna __ Anna Marabotti, Ph.D. Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with the gun is a dead

[gmx-users] R: Re: H-bond lifetime with g_hbond

with g_hbond To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4e9451dc.6010...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear gmx-users, I have a protein with 5 different ligands. For each system I made 30ns simulation and I calculated

[gmx-users] about periodic image minimum distance

looking at the system BEFORE simulation is made (and time is wasted...), and if it depends on some incorrect setting of the system (maybe some .mpd option?), or not. Thank you very much for your answers. Anna Anna Marabotti, Ph.D. Laboratory

[gmx-users] problem in topology with AMBER99SB

are not in correct order? Could you please help me? Many thanks Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39

[gmx-users] R: R: Re: g_cluster error in rhombic dodecahedric system

; charset=ISO-8859-1 Hi Anna, On Thu, Jul 21, 2011 at 5:11 PM, Anna Marabotti anna.marabo...@isa.cnr.it wrote: Thanks Mark for suggestion, I'll try to do a simpler clustering method. In the meantime, I only would like to add a further info: I pre-processed my trajectory following someone's (Justin

[gmx-users] g_cluster error in rhombic dodecahedric system

to manage it. Could the .tpr file I used be the cause of the problem? Could anybody help me please? Thank you so much for your continue support Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology

[gmx-users] R: Re: g_cluster error in rhombic dodecahedric system (Mark Abraham)

users gmx-users@gromacs.org Message-ID: 4e2836bf.3000...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 21/07/2011 11:38 PM, Anna Marabotti wrote: Hi folks here I am with another kind of error, this time analysing my trajectory of the rhombic dodecahedron dimeric system

[gmx-users] rhombic dodecahedron and g_sas

true? What can I do? Do I have to convert my trajectory into a rectangular one? Do I have to forgot to calculate SASA in these conditions? Any help will be appreciated... Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics

[gmx-users] R: Re: rhombic dodecahedron and g_sas

you're using a .gro file as a reference, which contains no charges. As a consequence, all atoms are taken to have zero charge, and thus regarded hydrophobic. Cheers, Tsjerk On Wed, Jul 13, 2011 at 2:35 PM, Anna Marabotti anna.marabo...@isa.cnr.it wrote: Dear all, once again about this subject

[gmx-users] R:Re: R: Re: g_mindist on rhombic dodecahedron system

Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear Justin, dear all, following your suggestion I used the command: trjconv -f prot_boxdodfull.xtc -s prot_boxdodfull.tpr -pbc mol -ur compact -o prot_boxdodfull_mol.xtc to convert my simulations, and as you

[gmx-users] R: Re: g_mindist on rhombic dodecahedron system

-0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re: g_mindist on rhombic dodecahedron system To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4e133aab.1030...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear

[gmx-users] R: g_mindist on rhombic dodecahedron system

Dear users, can anybody give me suggestions about my questions below? Thank you very much Anna _ Da: Anna Marabotti [mailto:anna.marabo...@isa.cnr.it] Inviato: lunedì 4 luglio 2011 17.43 A: 'gmx-users@gromacs.org' Oggetto: g_mindist on rhombic dodecahedron system Dear users

[gmx-users] Re: Re: g_mindist on rhombic dodecahedron system

on rhombic dodecahedron system To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4e133aab.1030...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear Tsjerk, thank you very much for your answer. I completely re-analyzed my simulations

[gmx-users] g_mindist on rhombic dodecahedron system

__ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it Skype account: annam1972 Web site

[gmx-users] R: gmx-users Digest, Vol 86, Issue 183

result in an altered ensemble, yet one in which you wouldn't see violations of the minimal distance. In a rhombic dodecahedron the spatial distribution is much more uniform... Cheers, Tsjerk On Mon, Jun 27, 2011 at 12:48 PM, Anna Marabotti anna.marabo...@isa.cnr.it wrote: Dear gmx-users, I'm

[gmx-users] about periodic image violations

Sorry, I forgot to change the subject of my previous mail. Anna -Messaggio originale- Da: Anna Marabotti [mailto:anna.marabo...@isa.cnr.it] Inviato: martedì 28 giugno 2011 12.09 A: 'gmx-users@gromacs.org' Oggetto: R: gmx-users Digest, Vol 86, Issue 183 Dear Tsjerk, dear all, thank you

[gmx-users] about periodic images violation

Dear gmx-users, I'm inserting into the discussion about periodic images since I'm experimenting a problem of minimum distance violation too. I'm doing simulations on a dimeric protein (with no covalent bonds between the two subunits) which derives not from a crystallographic structure but from a

[gmx-users] problem in gmx-users list archive?

Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo...@isa.cnr.it Skype account: annam1972 Web page: http

R: Re: [gmx-users] simulation of a peptide anchored to a support

=iso-8859-1 On 19/05/2011 7:09 PM, Anna Marabotti wrote: Dear gmx-users, I would like to simulate the conformational behaviour of a peptide covalently anchored to a rigid support with its N- and C-ter. I'm not interested in simulating the support, so I wonder if there is a way to simulate

R: Re: [gmx-users] numbering of .gro file

:54:38 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] numbering of .gro file To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4dcd381e.1020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear Mark, thank you

[gmx-users] numbering of .gro file

__ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm

R: Re: [gmx-users] numbering of .gro file

-users] numbering of .gro file To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4dcd2471.3020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear gmx-users, I'm simulating a homodimeric protein obtained by homology modelling

[gmx-users] R: gmx-users Digest, Vol 85, Issue 101

of .gro file To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 7690ae4b5380.4dcdb...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 13/05/11, Anna Marabotti anna.marabo...@isa.cnr.it wrote: Dear gmx-users, I'm simulating a homodimeric protein obtained

Re: [gmx-users] numbering of .gro file

Sorry I forgot to change the subject of my previous mail (see below) Anna -Messaggio originale- Da: Anna Marabotti [mailto:anna.marabo...@isa.cnr.it] Inviato: venerdì 13 maggio 2011 15.49 A: 'gmx-users@gromacs.org' Oggetto: R: gmx-users Digest, Vol 85, Issue 101 Dear Mark, thank you

[gmx-users] R: Md continuation with cpt

-grained (the sampling was every 5 steps) .edr file in which I could see that the energy values are stable. Any suggestions on this point? Many thanks and best regards Anna -Messaggio originale- Da: Anna Marabotti [mailto:anna.marabo...@isa.cnr.it] Inviato: giovedì 28 aprile 2011 16.55

[gmx-users] R: Md continuation with cpt

continuation with cpt To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4db833db.4050...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear gmx-users, since I'm sending my simulations to a system with a queue with a wallclock time of 24 h

[gmx-users] R: Md continuation with cpt

Subject: Re: [gmx-users] R: Md continuation with cpt To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4db947c0.90...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/28/2011 5:47 PM, Anna Marabotti wrote: Dear Justin, thank you for your precious help

[gmx-users] Md continuation with cpt

__ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it Skype account

[gmx-users] ffbonded.itp file

, not to each others (no C-C bond) and that oxygen is linked only to sulphur (no O-C bond). Could you please check for these strange interactions, or am I mistakenly interpreting them? Thank you very much and best regards Anna Marabotti -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] R: Re: adding a new residue in the ff

Dear Justin and Tsjerk, thank you very much for your last encouraging words...;-) I don't remember a time in my life where something that I needed, which was very complex to do, was already available...(apart from Gromacs package, of course!) About parameterization: sure I was intended to use the

[gmx-users] adding a new residue in the ff

generally to manage correctly the whole problem? Thanks a lot Anna Marabotti __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651

[gmx-users] LINCS warning on galactose molecule

hints about my problem? Or could it be a problem of galactose topology? Thank you very much and best regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via

[gmx-users] .cpt and .trr files

the precision of the result)? At present I'm keeping he .trr files (which contains all information) only to be sure I can restart a simulation, but I need DESPERATELY free disk space... Thank you very much Anna __ Anna Marabotti, Ph.D

[gmx-users] disulfide bridge broken during EM

and best regards Anna Marabotti PS BTW: often when I'm searching in the gmx-users list I see the suggestions to some links (for example in the message in http://lists.gromacs.org/pipermail/gmx-users/2008-March/032662.html Mark Abraham suggests to explore http://wiki.gromacs.org/index.php

[gmx-users] Re: disulfide bridge broken during EM

: 4d78ce62.2010...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear all, I have a PDB file of a protein that is in dimeric form, with an INTERchain disulphide bridge. However, in their paper the crystallographers are not sure if this is a true

[gmx-users] where to insert a new include DPOSRES in topology file?

__ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it Skype account: annam1972 Web

[gmx-users] R: gmx-users Digest, Vol 82, Issue 113

residues. It does. But it does not allow numbers higher than . Thus, with more residues, it will start counting over. Cheers, Tsjerk On Mon, Feb 14, 2011 at 4:52 PM, Anna Marabotti anna.marabo...@isa.cnr.it wrote: Dear Tsjerk, thank you very much. I really didn't know that the PDB format

[gmx-users] visualizing more than 9999 residues....

. I searched for some hints in the gmx-user list and in Google but I didn't find anything. Thank you very much and sorry for this off-topic question. Anna Marabotti __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics

[gmx-users] R: visualizing more than 9999 residues...

and segment identifiers to give all residues unique markers. Cheers, Tsjerk On Mon, Feb 14, 2011 at 4:29 PM, Anna Marabotti anna.marabo...@isa.cnr.it wrote: Dear gmx-users, I have a system formed by protein+ligand+lipid bilayer that accounts for about 10500 residues (56000 atoms). It seems to me

[gmx-users] protein+ligand+membrane: which forcefield?

forcefield instead? I did not understand if the Gromos 53a6 ff was chosen in the tutorial because it is better than 43a1 to manage such systems, or because it is more compliant than 43a1 with Berger lipids parameters. Many thanks for suggestions and best regards. Anna Marabotti -- gmx-users mailing

[gmx-users] segmentation fault while running eneconv

to concatenate my .edr files? Many thanks in advance and best regards Anna Marabotti Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825

[gmx-users] Re: segmentation fault while running eneconv

-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear all, I launched on my system a first simulation of 5 ns, then I prolonged it to 50 ns using tpbconv -s tpr1_5ns.tpr -until 5 -o tpr2_50ns.tpr and then mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt

[gmx-users] R: problem with .edr file

in advance and best regards Anna Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo

[gmx-users] problem with .edr file

in advance and best regards Anna Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo...@isa.cnr.it

[gmx-users] initial velocities analysis

at the .log file but I didn't find the information. g_traj generated a very big file, and presently I have some problems to analyze it. How can I see initial velocities? Many thanks and best regards Anna Anna Marabotti, Ph.D. Laboratory

[gmx-users] Re: stepsize too small: help to solve problem in GROMACS installation

Dear Justin, dear all, sorry for not having seen the warning before asking the question about compilers (just a little justification, however: the warning appears only on the Download page, not on the Installation page; I went directly to the installation page and I did not notice it). The only

[gmx-users] Re: stepsize too small: help to solve problem in GROMACS installation

: fbd7c308e524.4bfea...@anu.edu.au Content-Type: text/plain; CHARSET=US-ASCII - Original Message - From: Anna Marabotti anna.marabo...@isa.cnr.it Date: Thursday, May 27, 2010 16:55 Subject: [gmx-users] Re: stepsize too small: help to solve problem in GROMACS installation To: gmx-users@gromacs.org

[gmx-users] stepsize too small: help to solve problem in GROMACS installation

Could anybody of you help us for the debugging of this installation? Many thanks again and best regards Anna Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100

[gmx-users] Re: stepsize too small ... but potential energ negative!

...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear Justin, dear Luca, here's the answer to your questions: - I'm currently using the classical forcefield gromos96 43a1 (choice 0 in pdb2gmx). After producing the topology, the only warning I see from

[gmx-users] Re: stepsize too small ... but potential energy negative!

again thank you very much and best regards Anna Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email

[gmx-users] Re: stepsize too small ... but potential energy negative!

on my problem. I also want to thank Luca Mollica for his precious support during these days. Best regards Anna -Messaggio originale- Da: Justin A. Lemkul [mailto:jalem...@vt.edu] Inviato: martedì 25 maggio 2010 15.28 A: Anna Marabotti Oggetto: Re: R: coordinates and topologies of file

[gmx-users] stepsize too small ... but potential energy negative!

Dear Luca, dear all, thank you for your hints. I made some trials with my systems and these are my answers to your questions: - my system is a protein (with or w/o ligand) in solvent (water SPC). Following your suggestions, I tried to perform an EM on the protein w/o ligand after the editconf

[gmx-users] Re: stepsize too small ... but potential energy negative!

Dear Justin, dear Luca, here's the answer to your questions: - I'm currently using the classical forcefield gromos96 43a1 (choice 0 in pdb2gmx). After producing the topology, the only warning I see from pdb2gmx is this one: WARNING: there were 0 atoms with zero occupancy and 63 atoms with

[gmx-users] stepsize too small ... but potential energy negative!

don't think it's a problem related to the ligand. What do you think about? Could you give me some hint? Thank you very much and best regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology

[gmx-users] Re: minimizing ligand only

jalem...@vt.edu Subject: Re: [gmx-users] minimizing ligand only To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4bf16f19.5000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear gmx-users, is it possible to minimize a ligand

[gmx-users] minimizing ligand only

understand what to do. Many thanks in advance and best regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651

[gmx-users] MD localized in the active site

anything. Could anybody give me some suggestions about this subject, please? Many thanks in advance and regards. Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via

[gmx-users] Re: Re: problems running REMD on grids

Anna Marabotti wrote: Dear gmx-users, after a lot of trial (and errors) I finally got my REMD simulation. The problem was solved essentially when we avoided indicating the extension of the .tpr files: i.e. mdrun -s REMD_.tpr -multi 16 -replex 1000 -deffnm REMD_ -np 16 did not work, whereas

[gmx-users] Re: problems running REMD on grids

Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo...@isa.cnr.it Skype account: annam1972 Web

[gmx-users] Re: problems running REMD on grids

] problems running REMD on grids To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: cc9e9af0-0bd9-42a3-b81a-e51d4e47f...@rug.nl Content-Type: text/plain; charset=utf-8 Did you try to remove the _ from your file name? On Sep 11, 2009, at 14:04, Anna Marabotti anna.marabo...@isa.cnr.it

[gmx-users] R: problems running REMD on grids

I'm re-sending the message below because it seems to me that it has not arrived to the list. Please forgive me in case of duplicate sending. Best regards Anna _ Da: Anna Marabotti [mailto:anna.marabo...@isa.cnr.it] Inviato: venerdì 11 settembre 2009 14.05 A: 'gmx-users@gromacs.org

[gmx-users] problems running REMD on grids

as it was possible in the past. How can I find information in the GROMACS archives? Many thanks and regards Anna Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy

[gmx-users] using GROMACS in SDS-water simulations

for help and best regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabo

[gmx-users] Re: Re: protein in SDS/water

everything I need, but it would be nice that they could at least suggest me a solution in a less cryptic way when I have such a trivial problem, so I can avoid boring the developers themselves...;-) Thank you to all for collaboration and best regards Anna Anna Marabotti wrote: Dear all, as requested

[gmx-users] Re: protein in SDS/water

please if you need to see it let me know how to send to you. __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825

[gmx-users] Re: protein in SDS/water

Protein 1 SOL 36173 SDS 2000 I hope __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825

[gmx-users] Re: protein in SDS/water

genbox did not create by itself all corrections necessary to the original .top file when I used the -ci -nmol options? I added the -p flag but it doesn't change the topology by itself (as it should do, in my opinion). Thank you again Anna __ Anna

[gmx-users] Re: trouble for old/new GROMACS site

know if I'm the only person with this difficulty, could you please check it? Thanks anyway for the link and regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100

[gmx-users] trouble for old/new GROMACS site

to see the content of the site, and I did it, but still I don't see anything in the two sites. Can anyone help me? Thank you Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64

Re: [gmx-users] in vacuo minimization of a multimeric protein

: 4a1567a5.5070...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear gmx-users, I'm trying to do a mild minimization on a homohexameric protein in vacuo. I used the following options in the em.mdp file: title = mild-mini cpp

[gmx-users] in vacuo minimization of a multimeric protein

-users list and delete pbc from the em.mdp, but the results are quite the same). I also changed ns_type to simple, without success. Have you got any suggestion? Thanks in advance Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational

[gmx-users] R: R: help with neighborsearching error

it. Thank you very much for your patience and help, and for your useful suggestions. Best regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39

[gmx-users] R: neighborsearching error

minimization and PR-MD (after minimization and after minimization and water removal). Please let me know if you need some other infos. Many thanks and best regards. Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute

[gmx-users] R: neighborsearching error

alone, without solvent, before submitting to GROMACS procedure, but nothing changed, again. I really do not have idea of how to proceed. Any suggestion will be really welcome! Anna Anna Marabotti wrote: I'm resending the message without attachments, since the previous one was filtered because

[gmx-users] R: help with neighborsearching error

febbraio 2009 16.33 A: Anna Marabotti; Gromacs Users' List Oggetto: Re: help with neighborsearching error Anna Marabotti wrote: Dear Justin, I hope you wouldn't mind if I contact you directly, but I think I cannot send you the requested .log file via the gmx-users list because the message

[gmx-users] question about .trr file

of space savings. Am I correct? Thank you and regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype

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