Re: [gmx-users] Acpype error

2011-04-12 Thread Alan Wilter Sousa da Silva
/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt

Re: [gmx-users] converting ILDN parameters to RB

2011-03-31 Thread Alan Wilter Sousa da Silva
x 4.5 and above. But I don't want to fuss about it. If to forget about GMX 4.0.x and below is the way, so it will be. Thanks, Alan On 31 March 2011 16:08, David van der Spoel wrote: > On 2011-03-31 15.27, Alan Wilter Sousa da Silva wrote: > >> Hi there, >> >> Since

[gmx-users] converting ILDN parameters to RB

2011-03-31 Thread Alan Wilter Sousa da Silva
V[period] C[2] -= 4 * V[period] C[4] += 4 * V[period] So, as you can see, I can handle up to 4 periods (C[5] is always 0, but not with ILDN and I need to add C[6] rules as well). Any ideas? Many thanks in advance, Alan -- Alan Wilter SOUSA da SI

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

2011-01-06 Thread Alan Wilter Sousa da Silva
.0 0.0 A 3.39967e-01 >> 3.59824e-01 ; 1.91 0.0860 >> >> >> >> ... cc 0.0 0.0 A 3.39967e-01 >> 3.59824e-01 ; 1.91 0.0860[snip] >> >> Then, running grompp, I got several warnings, e.g.: >> >> WARNI

Re: [gmx-users] amber convert gromacs input files

2010-12-24 Thread Alan Wilter Sousa da Silva
-4 scaling). > > There may be other issues I'm not aware of yet. :) > > All the best, > Oliver > > > On 23 December 2010 18:13, Alan Wilter Sousa da Silva > wrote: > >> Have a look at acpype.googlecode.com >> >> Alan >> >> 2010/12/23

Re: [gmx-users] amber convert gromacs input files

2010-12-23 Thread Alan Wilter Sousa da Silva
users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Supp

[gmx-users] please, how edr data is xdr packed?

2010-08-22 Thread Alan Wilter Sousa da Silva
Hi there, I am trying to use python xdrlib module to read edr files but not knowing how the data is packed using the xdr protocol makes my work very difficult, if not impossible. Would someone kindly tell me how data is packed in the edr file? Or where it is the gromacs code so I can try to figur