Re: [gmx-users] do_dssp crashes on certain machines..

[EMAIL PROTECTED] wrote: Dear community, I have the following problem with do_dssp, when I try analysing a long 70 ns trajectory produced by a REMD calculation. All my previous analysis went fine, when the trajectory had a length of ~= 50ns. However, I now obtain the following errror message,

Re: [gmx-users] do_dssp crashes on certain machines..

hi, On Thursday, 19. April 2007 17:23, Mark Abraham wrote: [EMAIL PROTECTED] wrote: Dear community, I have the following problem with do_dssp, when I try analysing a long 70 ns trajectory produced by a REMD calculation. All my previous analysis went fine, when the trajectory had a

[gmx-users] do_dssp

Dear Gromacs users, As I am simulating many peptides in a box and do_dssp is only a wrapper for calling the program which works on pdb files, I was of the view that it will not take PBC into consideration and will probably not assign beta sheets very well. Please correct me if I am wrong. If

Re: [gmx-users] do_dssp

singh wrote: Dear Gromacs users, As I am simulating many peptides in a box and do_dssp is only a wrapper for calling the program which works on pdb files, I was of the view that it will not take PBC into consideration and will probably not assign beta sheets very well. Please correct me if I am

[gmx-users] do_dssp

Dear Gromacs users, I have simulated 12 peptide fragments in a cubic box and I want to use do_dssp for secondary structure analysis but I am not sure whether Periodic boundary conditions will be taken in account during assignment (particularly for assigning betasheets). Regards,

[gmx-users] do_dssp, -map option

Dear users, I would like to have some delucidations about the -map option of the do_dssp routine. In the help file, it says File that maps matrix data to colors, and I guess it is an input file to be supplied in order to assign colors to the different ss elements. Is it right? And, if so, how

[gmx-users] do_dssp with no output!

I have the same problem. Any suggestion??? DSSP variable is setup correctly, but nothing happens when I run do_dssp. It just freeze as Elena described. Thanks in advance, César.- ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] do_dssp : ssdump data

Where can I find the exhaustive list of one letter codes used from secondary structures? (H for helix, T for turn...) I looked at do_dssp.c to figure it out . the array map[]... semes to hold the relevant information, but I got very confused. Any help would be appreciated... Senthil

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:

Re: [gmx-users] do_dssp error

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, JahanMiguel Ortiz Lombardia [EMAIL PROTECTED] wrote: -BEGIN PGP SIGNED MESSAGE-Hash: SHA1Hi Jahan,First, you must make

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