From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Thu Jun 20 2013 - 11:25:52 CDT

From: flavio seixas <oivalf_nix_at_yahoo.com> To: nathan.li17_at_gmail.com Sent: Wednesday, June 19, 2013 11:57 PM Subject: Re: vmd-l: PSF not generating Hi. Yes. There are some servers that generate topology and parameter files. I use to try www.swissparam.ch You will find detailed instructions there. You can download the .mol2 file format of your ligands at zinc database and submit to swissparam. Special attention to the protonated state of ligands at pH 7.0 Regards, Flavio ------------------------------ Em qua, 19 de jun de 2013 16:48 GMT+01:00 Nathan Li escreveu: >Hi, > >Thanks for your response. Is there any automated way to generate the >topology files or do I have to manually create the CHARMM file? > >Thanks, >Nathan > > >On Tue, Jun 18, 2013 at 6:58 PM, flavio seixas <oivalf_nix_at_yahoo.com> wrote: > >> It seems you are not using topology files for the ligands PYP and 3DR >> Try to generate them and include they in the psf generator script. >> >> Regards, >> >> ------------------------------------- >> Flavio Augusto Vicente Seixas >> Laboratory of Structural Biochemistry >> Department of Biochemistry >> Universidade Estadual de Maringá, PR, Brazil >> http://www.uem.br >>  ------------------------------ >>  *From:* Nathan Li <nathan.li17_at_gmail.com> >> *To:* vmd-l_at_ks.uiuc.edu >> *Sent:* Tuesday, June 18, 2013 2:53 PM >> *Subject:* vmd-l: PSF not generating >> >> Hi all, >> >> I'm fairly new to VMD and just finished the tutorial. I'm trying to >> generate a PSF file for the following file, but it's not recognizing some >> of the bonds and atoms. >> http://www.rcsb.org/pdb/explore/explore.do?structureId=1FZL >> >> Any help would be greatly appreciated. >> Thanks! >> >> -- >> >> Nathan Li >> Pratt School of Engineering, Duke University 2014 >> 678-467-5421 >> nathan.li_at_duke.edu >>