Re: [gmx-users] Acpype error

2011-04-12 Thread Alan Wilter Sousa da Silva
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 - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing list

[gmx-users] converting ILDN parameters to RB

2011-03-31 Thread Alan Wilter Sousa da Silva
] 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 SILVA, DSc

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

2011-03-31 Thread Alan Wilter Sousa da Silva
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 sp...@xray.bmc.uu.se wrote: On 2011-03-31 15.27, Alan Wilter Sousa da Silva wrote: Hi there, Since ILDN dihedrals has some

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

2011-01-06 Thread Alan Wilter Sousa da Silva
Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Alan Wilter SOUSA da SILVA, D.Sc. Bioinformatician, UniProt - PANDA, EBI-EMBL CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

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

2010-12-24 Thread Alan Wilter Sousa da Silva
2010 18:13, Alan Wilter Sousa da Silva awil...@ebi.ac.ukwrote: Have a look at acpype.googlecode.com Alan 2010/12/23 gromacs564 gromacs...@126.com Hi , I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam web(they are glycam06 force field,included in AMBER

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

2010-12-23 Thread Alan Wilter Sousa da Silva
/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/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, D.Sc. Bioinformatician, UniProt - PANDA, EBI-EMBL

[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