Re: [gmx-users] protein/dmso simulation

2008-08-19 Thread Bhanu
Try "genbox -cp *.gro -ci dmso.gro -p *.top -o *.gro" Gro file for dmso comes built-in with gromacs 3.3. As Justin has directed, forcefields do matter. On 19/08/2008, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > > prasun kumar wrote: > >> dear users >> I am trying to run the simulation fo a

[gmx-users] dmso/peptide simulation

2008-08-19 Thread prasun kumar
I am using the forcefield 43a2 option number 2 ie improved alkane dihedrals and i am using the same dmso.gro and dmso.itp file that is given in the share/top file of gromacs.but it is also right that the atom names are not matching in rtp file. I tried by replasing SDmso by SD in rtp file its not

Re: [gmx-users] Re:Error in trjconv

2008-08-19 Thread Tsjerk Wassenaar
Hi Parthiban, Well, it was the best possible shot in the dark. Then please enlighten us with more information: What is your command line? What platform do you use? Which compiler? When did it work? What system? Cheers, Tsjerk On Tue, Aug 19, 2008 at 5:55 AM, M.Parthiban <[EMAIL PROTECTED]> wrot

[gmx-users] Re: protein/dmso simulation

2008-08-19 Thread Vitaly Chaban
> prasun kumar wrote: >> dear users >> I am trying to run the simulation fo a protein/DMSO system,Its working >> well till genbox but while running GROMPP I am gettin a fatal >> error,which is >> atom type 'SD' not found. >> SD is given in the gro & itp file of DMSO. >> what should I do to overcome

Re: [gmx-users] Re: gmx-users Digest, Vol 52, Issue 66

2008-08-19 Thread Tsjerk Wassenaar
Please also note that *do_dssp* is part of the gromacs suite, and is basically a wrapper around the third-party program *dssp* from CMBI, calling it for every frame and processing the output. do_dssp relies on the environment variable DSSP for locating dssp. Tsjerk On Mon, Aug 18, 2008 at 9:07 PM

[gmx-users] charmm and oplsaa simulation results don't match

2008-08-19 Thread sarbani chattopadhyay
  Hi everybody, I had run a long 100ns simulation on a tripeptide using opls/aa force field and spc water model. I got a few microstates. Then I tried to run simulation on the same system using charmm force field and tip3p water model. However I couldn't find the microstate

[gmx-users] Re: gmx-users Digest, Vol 52, Issue 77

2008-08-19 Thread M.Parthiban
hi trjconv_mpi -f dimer_md.trr -o dimer_md.xtc (command which i used) Linux (Platform) Cluster machine (30 nodes, 1 node = 4 processor) again i want you to know that my molecule is dimer with a small ligand which gives error. my molecule alone dosent gives error thanks Parthiban > Hi Parthiban

[gmx-users] Error in trjconv

2008-08-19 Thread M.Parthiban
hi trjconv_mpi -f dimer_md.trr -o dimer_md.xtc (command which i used) Linux (Platform) Cluster machine (30 nodes, 1 node = 4 processor) again i want you to know that my molecule is dimer with a small ligand which gives error. my molecule alone dosent gives error thanks Parthiban > Hi Parthiban

[gmx-users] dmso/peptide simulation

2008-08-19 Thread prasun kumar
I have already included the dmso.itp file.still I am getting the error atom type SD not found thanx in advance for helping me -- PRASUN (ASHOKA) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] dmso/peptide simulation

2008-08-19 Thread Justin A. Lemkul
prasun kumar wrote: I have already included the dmso.itp file.still I am getting the error atom type SD not found thanx in advance for helping me I don't know why (grompp?) is looking for atom type SD, when the atom *type* is SDmso, but the atom *name* is SD. Are you sure you have made no

[Fwd: Re: [gmx-users]build topology file for a molecule define with new residues]

2008-08-19 Thread cilpa
Hi all, Is anybody has already done umbrella sampling for a free energy calculation? There are some theoretical documentation but not so much information on how to do that in practice. For me it's the first time. could anybody know how for pulling or approaching two biomolecules and step simulation

Re: [gmx-users] Error in trjconv

2008-08-19 Thread Tsjerk Wassenaar
Ah, sure, now we know! Well, actually I almost confirmed my suspicion, just searching for libc.so.6 in the archives. But first, you might want to read http://www.catb.org/~esr/faqs/smart-questions.html Then, you can continue with http://www.gromacs.org/pipermail/gmx-users/2007-November/030605.html

Re: [Fwd: Re: [gmx-users]build topology file for a molecule define with new residues]

2008-08-19 Thread Justin A. Lemkul
[EMAIL PROTECTED] wrote: Hi all, Is anybody has already done umbrella sampling for a free energy calculation? There are some theoretical documentation but not so much information on how to do that in practice. For me it's the first time. could anybody know how for pulling or approaching two bio

[gmx-users] Re: temperature coupling for complex+ligand+water+ions

2008-08-19 Thread Alan
Thanks Justin for your reply. In fact I did look that references and discussion you mentioned and actually my e-mail was induced by them because I wanted to put some conclusions in a straight bottom line. I've been even reading Amber manual about their implementation for pressure and temperature c

[gmx-users] Re: gmx-users Digest, Vol 52, Issue 78

2008-08-19 Thread Vitaly Chaban
> I have already included the dmso.itp file.still I am getting the error > atom type SD not found > thanx in advance for helping me So everything should work. Either you didn't include corresponding topology or you included something else to conflict. Start your pursue from the very beginning. Ty

[gmx-users] RE: [ atomtypes ] are not case sensitive?

2008-08-19 Thread Alan
Dear Berk, Thanks for your attention. I don't know how familiar are you to amb2gmx and ffamber port to GMX. I am just learning since I am trying to test an application that is related to amb2gmx and ffamber (acpypi). So, for Amber MD (MD to contrast with FF), Generalised Amber Force Field (GAFF)

Re: [gmx-users] Re: temperature coupling for complex+ligand+water+ions

2008-08-19 Thread Justin A. Lemkul
Alan wrote: Thanks Justin for your reply. In fact I did look that references and discussion you mentioned and actually my e-mail was induced by them because I wanted to put some conclusions in a straight bottom line. I've been even reading Amber manual about their implementation for pressur

Re: [gmx-users] dmso/peptide simulation

2008-08-19 Thread Anil Kumar
Hi, You are on the right track .actually the problem lies with dmso.itp which comes with original gromacs package...in that one column of mass is missing just after column of charge value...so you just add them and then it will work fine. (For hint you go through meoh.itp!) with regards anil

RE: [gmx-users] RE: [ atomtypes ] are not case sensitive?

2008-08-19 Thread Berk Hess
Hi, I don't know if any thinking went into the (non) case specifity of atom types. Nearly all string comparisons in Gromacs are not case specific. For things like atom names this makes sense. We could change the atom type comparisons to case specific. I think that all force field files supplied w

Re: [Fwd: Re: [gmx-users]build topology file for a molecule define with new residues]

2008-08-19 Thread cilpa
thank you, check the site given in the post but there's no tutorial but i least the dissertation of the guy doing those calculations, i could check that. thanks for suggesting me geraldine On Tue, August 19, 2008 1:15 pm, Justin A. Lemkul wrote: > > > [EMAIL PROTECTED] wrote: >> Hi all, >> Is a

[gmx-users] charmm and oplsaa simulation results don't match

2008-08-19 Thread Chris Neale
If a user could be assured that they would obtained the same microstates, even in an infinite simulation, then we could finally get rid of the multitude of ff's and pick 'one' since they would all agree. However, this is not the case. Therefore your assumption that you *should* get the same answe

FW: [gmx-users] charmm and oplsaa simulation results don't match

2008-08-19 Thread Berk Hess
From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: RE: [gmx-users] charmm and oplsaa simulation results don't match Date: Tue, 19 Aug 2008 10:47:02 +0200 Hi, There are two main issues here. One is sampling. I don't know what the correlations times in your systems are. You say you o

Re: FW: [gmx-users] charmm and oplsaa simulation results don't match

2008-08-19 Thread sarbani chattopadhyay
hi,   Thanks for the suggestions. Actually the microstates are revisited in the 100ns span and one of them is occupied for longer time span than the others. I had broken the 100ns trajectory(oplsaa) in 3 parts and took starting structures from each of them and run simulations and obtained comp

[gmx-users] Questions about brownian/langevin dynamics of bead-spring polymers

2008-08-19 Thread Suman Chakrabarty
Dear all, I have just started learning gromacs to implement on a bead-spring polymer system mainly to study hydrophobic collapse. While I am going through the manual in detail, I have the following questions/confusions. 1. Which force field would be best to study such a system? Currently I am us

[gmx-users] Help with grompp with amber99 forcefield

2008-08-19 Thread Ragnarok sdf
Hello, I've searched the archives in search of an answer for my problem and was able to solve only part of the problem. I am working with a DNA/Protein system with AMBER99 forcefield. The first problem is "...Generated 2628 of the 2628 non-bonded parameter combinations Generating 1-4 interactions:

[gmx-users] charmm and oplsaa simulation results don't match

2008-08-19 Thread Chris Neale
water is part of the ff, therefore see previous comments of Berk and myself. For a reference, see Ponder and Case 2003 (http://www.ncbi.nlm.nih.gov/pubmed/14631816), and while one of the pmfs that they present is quantitatively incorrect, the conclusions are valid: the different protein/water ff'

Re: [gmx-users] Help with grompp with amber99 forcefield

2008-08-19 Thread Justin A. Lemkul
Ragnarok sdf wrote: And the second error is the total system carge which is a non integral charge. I've looked for the " ERROR 0 [file "1VKX_C.itp", line 420]: No default Bond types" solution but no one seams to have had the same problem as I. Not entirely true, they just haven't had th

[gmx-users] Using Morse potentials with ENCAD force field

2008-08-19 Thread Andy Shelley
I have added a mixture of oxgen and nitrogen to a simulation with a cnt. The oxygen and nitrogen use morse potentials and the cnt uses the encad force field. Previously I simulated the cnt with the default water and it worked well. When using my "air" mixture the cnt collapses even if a small numb

[gmx-users] REMD trjcat -demux problem

2008-08-19 Thread Di Pan
Hi, everyone: I met a problem when I try to use the trjcat -demux to connect trajectory files of REMD. I use 68 replicas for REMD simulation, and use demux.pl script to get the replica_index.vgx file. Then I try to use the trjcat -f traj*.xtc -demux replica_index.xvg to get a continuous trajctory

[gmx-users] tfe.itp

2008-08-19 Thread shahrbanoo karbalaee
Dear justin I made topology top for tfe with gromos53a5.and I solvated in spc and 40molecule tfe.I includeed tfe.itp in topology.but when I do grompp I get this error.(I edit the name of atoms with name in rtp file HT) Generated 165 of the 1596 non-bonded parameter combinations ERROR 0 [file "topo

Re: [gmx-users] REMD trjcat -demux problem

2008-08-19 Thread David van der Spoel
Di Pan wrote: Hi, everyone: I met a problem when I try to use the trjcat -demux to connect trajectory files of REMD. I use 68 replicas for REMD simulation, and use demux.pl script to get the replica_index.vgx file. Then I try to use the trjcat -f traj*.xtc -demux replica_index.xvg to get a co

Re: [gmx-users] Using Morse potentials with ENCAD force field

2008-08-19 Thread David van der Spoel
Andy Shelley wrote: I have added a mixture of oxgen and nitrogen to a simulation with a cnt. The oxygen and nitrogen use morse potentials and the cnt uses the encad force field. Previously I simulated the cnt with the default water and it worked well. When using my "air" mixture the cnt colla