Re: [gmx-users] charmm27 in gromacs- grompp error
Sounds like either you're following wrong instructions, or not following them correctly. Please double check and/or take up the issue with the author. Mark On Wed, Jun 12, 2013 at 3:03 PM, Revthi Sanker wrote: > Dear all, > I am using charmm27 forcefield in gromacs for performing all atom > simulations (system comprising of DOPC, cholesteryl ester and protein) .I > got the itp file for dopc from the lipid book in which they have mentioned > #include "charmm27.ff/ffbonded.itp" and "charmm27.ff/ffnonbonded.itp" to > source to these for the parameters of each bond, angle dihedral etc based > on the atom types instead of mentioning explicitly each numerical value > from the gromacs directory.But it could not read the file and displayed: > > Syntax error - File ffbonded.itp, line 2 Last line read: '[ atomtypes ]' > Invalid order for directive defaults > > When I commented those lines and again ran grompp, it generated the > following error: > No default Angle types > No default Ryckaert-Bell. types. > > Kindly suggest me in this issue. > > Earnestly awaiting a reply, > > Revathi > M.S. Research Scholar > Indian Institute Of Technology, Madras > India > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] charmm27 in gromacs- grompp error
Dear all, I am using charmm27 forcefield in gromacs for performing all atom simulations (system comprising of DOPC, cholesteryl ester and protein) .I got the itp file for dopc from the lipid book in which they have mentioned #include "charmm27.ff/ffbonded.itp" and "charmm27.ff/ffnonbonded.itp" to source to these for the parameters of each bond, angle dihedral etc based on the atom types instead of mentioning explicitly each numerical value from the gromacs directory.But it could not read the file and displayed: Syntax error - File ffbonded.itp, line 2 Last line read: '[ atomtypes ]' Invalid order for directive defaults When I commented those lines and again ran grompp, it generated the following error: No default Angle types No default Ryckaert-Bell. types. Kindly suggest me in this issue. Earnestly awaiting a reply, Revathi M.S. Research Scholar Indian Institute Of Technology, Madras India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] charmm27 in gromacs
In a nutshell, yes dihedral type 2 is for the IMPR charmm dihedrals and 9 is for the normal dihedrals. I think David or someone else added code to specifically support charmm dihedrals in this way. On 2012-02-14 09:32:37PM -0600, Tom wrote: > Dear Gmx Developer or Users, > > Can anyone explain which section is for the parameters of improper > dihedral angle > on the file of ffbonded.itp ? > > On the file of ffbonded.itp, there is not any comment to differentiate the > proper and improper > dihedral angle. > > E.g. on thie file of ffbonded.itp in the directory of charmm27.ff > There are two sections about dihedral angle: > > [ dihedraltypes ] > ; i j k l funcphi0cp mult > C CT1 NH1 C * 9* 180.00 0.8368 1 > .. > > [ dihedraltypes ] > ; i j k l funcq0 cq > CPB CPA NPH CPA* 2* 0. 174.0544 > .. > There is also no explaination the explaination about the function type 2. > > It seems difficult for users to edit the parameters. > Thanks for the explainations! > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] charmm27 in gromacs
Tom wrote: Dear Gmx Developer or Users, Can anyone explain which section is for the parameters of improper dihedral angle on the file of ffbonded.itp ? On the file of ffbonded.itp, there is not any comment to differentiate the proper and improper dihedral angle. E.g. on thie file of ffbonded.itp in the directory of charmm27.ff There are two sections about dihedral angle: [ dihedraltypes ] ; i j k l funcphi0cp mult C CT1 NH1 C * 9* 180.00 0.8368 1 .. [ dihedraltypes ] ; i j k l funcq0 cq CPB CPA NPH CPA* 2* 0. 174.0544 .. There is also no explaination the explaination about the function type 2. Table 5.5 of the manual lists all function types, what they are, and what the required parameters are. Functional forms are discussed in section 4.2. It seems difficult for users to edit the parameters. Comprehensive explanations of all nuts and bolts are beyond what can be included in the manual or force field files. A deep knowledge of the underlying force field (which may span several published papers, other manuals, etc) is required to understand any of the force fields implemented in Gromacs (or any other software, for that matter). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] charmm27 in gromacs
Dear Gmx Developer or Users, Can anyone explain which section is for the parameters of improper dihedral angle on the file of ffbonded.itp ? On the file of ffbonded.itp, there is not any comment to differentiate the proper and improper dihedral angle. E.g. on thie file of ffbonded.itp in the directory of charmm27.ff There are two sections about dihedral angle: [ dihedraltypes ] ; i j k l funcphi0cp mult C CT1 NH1 C * 9* 180.00 0.8368 1 .. [ dihedraltypes ] ; i j k l funcq0 cq CPB CPA NPH CPA* 2* 0. 174.0544 .. There is also no explaination the explaination about the function type 2. It seems difficult for users to edit the parameters. Thanks for the explainations! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
