[gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file

Hi Justin I read through the beastly error file and did as you said. It worked! Just missed a few lines in the ffbonded.itp. Thank you -- View this message in context: http://gromacs.5086.n6.nabble.com/top-file-incoherent-with-the-values-in-the-ffbonded-itp-file-tp4998966p4998975.html Sent from

[gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file

Hi Justin I have changed all the force field parameters as below, (I have already shown my ffbonded.itp file) ffnonbonded.itp ; name bond_typemasscharge ptype sigma epsilon opls_966 CA612.01100 0.240 A3.5000e-01 3.3600e-01 opls_967 CA6

[gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file

Hi Justin Thank you for your reply. However, when I am using the grompp command, the topol.tpr file is not being formed due to a fatal error. This fatal error is the cumulative of ' No default Ryckaert-Bell.' types for many atoms in the polymer chain. Also, regarding the comment on the atom types a

[gmx-users] .top file incoherent with the values in the ffbonded.itp file

Hello My A.gro file is: 1PvB CB1 3.109 2.784 0.803 0. 0. 0. 1PvBHB12 3.156 2.880 0.843 0. 0. 0. 1PvBHB23 2.997 2.797 0.819 0. 0. 0. 1PvBHB34 3.129 2.765 0.693 0. 0. 0.

[gmx-users] Re: Regarding pdb file of a polymer

Hi Justin Thank you for the reply. I have got my answer and its clear now. Regards Sreeta On 19 June 2012 16:55, Justin A. Lemkul [via GROMACS] < ml-node+s5086n4998714...@n6.nabble.com> wrote: > > > On 6/19/12 4:49 PM, sreeta.g wrote: > > Hi Justin > > Thank you for th

[gmx-users] Re: Regarding pdb file of a polymer

ending groups as described in the tutorial (rather than the entire length of chain). Thank you Sreeta On 19 June 2012 15:46, Justin A. Lemkul [via GROMACS] < ml-node+s5086n499871...@n6.nabble.com> wrote: > > > On 6/19/12 3:17 PM, sreeta.g wrote: > > > Hi > > I am

[gmx-users] Regarding pdb file of a polymer

Hi I am working with Polyvinyl Alcohol polymer. I have been following http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html (procedure by Justin) this thread for a lot of guidance. I have obtained the coordinate file for PVA from other sources, however, I am unable to understand how