Re: [gmx-users] nucleic acis simulation

Hi Erik, Yep, the problem was indeed with the ifdefs... I'm sorry, I thought I had posted a solution. My bad. Miguel En/na Erik Marklund ha escrit: > Hi everyone. > > I found this old thread and noticed that Miguel Ortis Lombardia had the > same problems I had just half an hour ago. It seems

Re: [gmx-users] Re: gmx-users Digest, Vol 30, Issue 18

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi, Stefan, To the first question: (run in Ubuntu) > locate cpp | grep "/cpp$" /lib/cpp /usr/bin/cpp /usr/share/doc/cpp For the second, you must make sure that the atom names, for example, from your Prodrg topology are compatible with those in the f

Re: [gmx-users] gromacs parallel doesn't work

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Beniamino, Perhaps you upgraded/updated your system kernel and for some reason didn't choose the smp-enabled kernel. If the update/upgrade is done automatically, check that its parameters are well chosen. Also, if you don't use it, remove any kerne

Re: [gmx-users] gromacs parallel doesn't work

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Beniamino, No, you should see a line: processor : 1 together with its full description. Your output means your system sees a single processor. Looks like a hardware problem, then. HTH, Miguel En/na Beniamino Sciacca ha escrit: > [EMAIL

Re: [gmx-users] 2 beginner´s questions

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi, I like a lot "chimera" (http://www.cgl.ucsf.edu/chimera/) It doesn't currently support gromacs trajectories, but it does support trajectories exported to single or multiple pdb files. It's incredibly easy to learn and use. You can depict your mole

Re: [gmx-users] do_dssp error

t; Thanks for your reply. > I used from Gromacs on WindowsXP with command prompt. How can I change > DSSP path in this environment? Thank you very much. > > Sincerely yours, > Jahan > > */Miguel Ortiz Lombardia <[EMAIL PROTECTED]>/* wrote: > > Hi Jahan, > >

Re: [gmx-users] do_dssp error

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Jahan, First, you must make sure you have the dssp program; it doesn't come with gromacs, but you can download it separately from: http://swift.cmbi.ru.nl/gv/dssp/ Secondly, if 'setenv' is not working you are not on a csh/tcsh shell. Try: export

Re: [gmx-users] Orientation restraints

Hi Bob, Just a comment: if you don't have a homogeneous DNA sequence (and perhaps even in such a case) you will probably end distorting the sugar-phosphate backbone of the DNA if forcing every base pair to be normal to a common z-axis. Anyway, look for one of these two programs: freehelix (by Di

Re: [gmx-users] genion in gromacs 3.3.1

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 > >> You can try -norandom. I was under the impression that the potential >> based placement was broken (had been for a while). > > Hi David, Thank you very much, the command line option -norandom did work and placed the cations in the same place as

[gmx-users] genion in gromacs 3.3.1

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear colleagues, It looks like genion behaviour has changed in gromacs 3.3.1 as compared to 3.3 I still have both binaries in my machine and when using identical inputs to add some Na cations the new one (3.3.1) adds them randomly, while the previous

Re: [gmx-users] bugzilla

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi David, It works for me. Miguel En/na David van der Spoel ha escrit: > David Mobley wrote: >> All, >> >> I can't connect to bugzilla.gromacs.org currently. Is it down? >> > works for me. > > can someone confirm that it works from off-site as wel

Re: [gmx-users] Not enough ref_t and tau_t values!

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Thank you Tsjerk. Indeed, you're right. I'm using ffamber99, where the terminal residues have names starting with N or C, for N- and C-terminal. After reading your e-mail I re-run make_ndx and noticed that these terminal residues are not considered Pr

Re: [gmx-users] Not enough ref_t and tau_t values!

g from one of my > groups. I made a new index.ndx file and no errors were reported anymore. > So my piece of advice is check your index file. I hope it helps, > greetings, > MGiò > > > On 3/7/06, *Miguel Ortiz Lombardia* <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]&g

[gmx-users] Not enough ref_t and tau_t values!

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi all, I get this error from grompp: Program grompp, VERSION 3.3 Source code file: readir.c, line: 1131 Fatal error: Not enough ref_t and tau_t values! However, I do have three values for ref_t and tau_t, as many as groups (I made an index.ndx fil

Re: [gmx-users] nucleic acis simulation

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 David van der Spoel escribió el 28/02/06 11:25 : > Miguel Ortiz Lombardia wrote: > Thank you Maik. > > The AMBER ports are some I'm testing, sure. > BTW, I can't get it ready if I solvate the model. Everything goes fine

Re: [gmx-users] nucleic acis simulation

tute for Biophysical Chemistry > Theoretical & 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:/

[gmx-users] nucleic acis simulation

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, This is a question from someone just taking some timid steps in this field. I'd like to know what force field, among those available in Gromacs (v. 3.3) would you consider "better" for models containing nucleic acids. As I understand this ma