Re: [gmx-users] How to use "gmx editconf -bf" to assign b-factor values to a PDB containing multiple frames?
Hi, Unfortunately there's no infrastructure for that, so you should either consider something like MDAnalysis, or resort to trjconv -dump to get single frames to give to editconf. Mark On Fri, Feb 2, 2018 at 2:02 PM ZHANG Cheng <272699...@qq.com> wrote: > Dear Gromacs, > I am using: > > > gmx editconf -f protein.pdb -bf bf.dat -o bf.pdb > > > to assign b-factor values to "protein.pdb", which contains multiple pdb > frames. However, the output "bf.pdb" only includes the first frame. > > > Can I ask is there a way to assign b-factor values to all the frames of > one pdb file? > > > Yours sincerely > Cheng > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to use "gmx editconf -bf" to assign b-factor values to a PDB containing multiple frames?
On 2/2/18 8:01 AM, ZHANG Cheng wrote: Dear Gromacs, I am using: gmx editconf -f protein.pdb -bf bf.dat -o bf.pdb to assign b-factor values to "protein.pdb", which contains multiple pdb frames. However, the output "bf.pdb" only includes the first frame. Can I ask is there a way to assign b-factor values to all the frames of one pdb file? Not within GROMACS. You'll have to write your own program or script to do this. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to use "gmx editconf -bf" to assign b-factor values to a PDB containing multiple frames?
Dear Gromacs, I am using: gmx editconf -f protein.pdb -bf bf.dat -o bf.pdb to assign b-factor values to "protein.pdb", which contains multiple pdb frames. However, the output "bf.pdb" only includes the first frame. Can I ask is there a way to assign b-factor values to all the frames of one pdb file? Yours sincerely Cheng -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
