Please try BUILD_METHOD = 'INTERNAL_COORDINATES', wherever BUILD_METHOD = '3D_INTERPOLATION' occurs in the script(s). If this does not help, please send me a sample problem.
> > This is a multi-part message in MIME format. > --------------D65A8975251E8BB9BC9BC0B2 > Content-Type: text/plain; charset=us-ascii > Content-Transfer-Encoding: 7bit > > Dear Andrej, > > I have again ( or additional) problems with MODELLER4. > I have added all H to short peptide from PBD using 'all_hydrogen.top' script > from examples directory but result is somehow strange. Some H's are 2.5A away > but some others only 0.5A from respective root atoms. It could be that it is problem > with my installation of MODELLER therefore I do not expect that you will work > on this (unless it is already recognized, general problem). However I will appreciate > some hints. > - What is logistic for adding hydrogens to heavy atoms? Formaly it is only > different library which I am using (top.lib instead of top_heav.lib) but what > happens in the program? > - What is the name of subroutine where H atom positions are calculated? > I think that something is going wrong in this subroutine. > Of course, if you want, I will inform you about results of my investigations. > > Kind regards, > Andrzej > > --------------D65A8975251E8BB9BC9BC0B2 > Content-Type: text/x-vcard; charset=us-ascii; name="vcard.vcf" > Content-Transfer-Encoding: 7bit > Content-Description: Card for Andrzej Sawaryn > Content-Disposition: attachment; filename="vcard.vcf" > > begin: vcard > fn: Andrzej Sawaryn > n: Sawaryn;Andrzej > org: Institute of Physics > adr: Ratzeburger Allee 160;;;Luebeck;;D-23538;Germany > email;internet: firstname.lastname@example.org > title: Dr. > tel;work: +49-451-5004203 > tel;fax: +49-451-5004214 > tel;home: Do not ditsurb me at home! > x-mozilla-cpt: ;0 > x-mozilla-html: TRUE > version: 2.1 > end: vcard > > > --------------D65A8975251E8BB9BC9BC0B2-- >