Hi, I fixed it for the next beta release. If you need it now, change on line 1574 (my latest version) of src/kernel/pdb2gmx.c cc->r_start to cc->r_end, or get the 4.5 version from git.
Berk Date: Tue, 24 Aug 2010 09:21:44 -0500 From: kkucz...@ku.edu To: gmx-users@gromacs.org Subject: [gmx-users] Incorrect C-terminal in peptide starting with GLY Hi gmx-users I am trying to set up a simulation of a 16-residue peptide that starts with GLY and ends with GLU (PDB attached) using OPLS-AA/L and gromacs-4.5-beta3. Here is the pdb2gmx command pdb2gmx -inter -ignh -f b-hp41-56.pdb -p peptide.top -o peptide.gro the ff, water, ionization state selection goes well, I get a selection of N-terminals that includes GLY-NH3+ which is fine but then the selection of C-terminals does not have COO-, but only GLY-COO- - as a result the C-terminal GLU ends up with incorrect charge and qtot is not an integer Without the '-inter', the system gets GLY-NH3+ and GLY-COO- as well ... Could someone suggest a fix for this ? Regards Krzysztof -- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.html -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
