cellulose builder structure and CHARMM36 force field
262 views
Skip to first unread message
Jaqueline Sousa
Jul 22, 2015, 2:53:01 PM7/22/15
to cellulose-builder
Dear developer,
I'm a undergrad student and I'm having trouble running the generated .pdb structure (a 12 5 10 parallelepiped) in gromacs with the CHARMM36 force field. Whenever I use pdb2gmx command to produce the .gro file, I keep getting messages of missing atoms. More specifically the HO4, HO1 and O1 atoms, which are actually expected to be missing since they're part of the glycosidic bonds. I understand from the article, that the topologies used are meant to work with the CHARMM force fields (though I'm not sure what version of it). Indeed the .rtp file of CHARMM36 have the atoms for the resiude BGLC but they seem to be for a simple beta-glucose residue, a monosaccharide. I've done a lot of reasearch and there seems to be a problem with CHARMM36 and gromacs, but at the same time CHARMM36 BGLC atoms include all those atoms that'll be naturally missing from a polysaccharide structure, so I'm not sure anymore if the problem has not to do with an incompatibility between cellulose-builder .pdb file and the CHARMM36 parameters.
Any help would be appreciated,
Jaqueline Sousa
PS: it ts really desirable to run the dynamics with Gromacs.
I'm a undergrad student and I'm having trouble running the generated .pdb structure (a 12 5 10 parallelepiped) in gromacs with the CHARMM36 force field. Whenever I use pdb2gmx command to produce the .gro file, I keep getting messages of missing atoms. More specifically the HO4, HO1 and O1 atoms, which are actually expected to be missing since they're part of the glycosidic bonds. I understand from the article, that the topologies used are meant to work with the CHARMM force fields (though I'm not sure what version of it). Indeed the .rtp file of CHARMM36 have the atoms for the resiude BGLC but they seem to be for a simple beta-glucose residue, a monosaccharide. I've done a lot of reasearch and there seems to be a problem with CHARMM36 and gromacs, but at the same time CHARMM36 BGLC atoms include all those atoms that'll be naturally missing from a polysaccharide structure, so I'm not sure anymore if the problem has not to do with an incompatibility between cellulose-builder .pdb file and the CHARMM36 parameters.
Any help would be appreciated,
Jaqueline Sousa
PS: it ts really desirable to run the dynamics with Gromacs.
Thiago Gomes
Aug 6, 2015, 6:57:16 PM8/6/15
to cellulos...@googlegroups.com
Dear Jacqueline,
I will have to go through GROMACS documentation to help you with that. That might take a while since I have been super busy, but I will get back to you when I´m ready. In cellulose-builder´s next version we intend to make it more straightforward to Gromacs users.
--
You received this message because you are subscribed to the Google Groups "cellulose-builder" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cellulose-buil...@googlegroups.com.
To post to this group, send email to cellulos...@googlegroups.com.
Visit this group at http://groups.google.com/group/cellulose-builder.
For more options, visit https://groups.google.com/d/optout.
Jaqueline Sousa
Aug 23, 2015, 10:58:16 PM8/23/15
to cellulose-builder
Thanks Thiago, Munir Skaf also answered me, and I thought I'd solved the problem by creating a new residue in the CHARMM ff files, but turned out parametrizing a force field is just not that simple, and my structure keeps clashing.
Abraços,
Abraços,
Jaqueline Sousa
Reply all
Reply to author
Forward
0 new messages