Re: [gmx-users] grompp erro
My question related to your choice at the N terminus. Your existing atoms seem to be a methylated amine, which you probably should not want to change. Mark On Jan 21, 2014 9:17 AM, Albert mailmd2...@gmail.com wrote: On 01/21/2014 12:46 AM, Mark Abraham wrote: Why are you trying to make a methylated amine into an NH2 via your choice of 1 for -ter? Mark yes, for the c-term. I delete the frist residue Thr from my pdb file, and the problem solved. It seems that this error related the Thr at n-term. best Albert -- 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] grompp erro
Here are the atoms mentioned in the log file: 1NH2 19THR N 1 -0.96 14.007 ; qtot -0.96 3CT1 19THR CA 4 0.19 12.011 ; qtot -0.09 4CT1 19THR CB 6 0.14 12.011 ; qtot 0.14 5HB1 19THR HA 5 0.09 1.008 ; qtot 0 On 01/19/2014 09:46 PM, Justin Lemkul wrote: OK, now please provide the rest of the information I asked for in my other email: What are those atoms and what are their types? Only you know what your topology is. Please make it easy and expedient to help us to help you! -Justin -- 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] grompp erro
On 01/19/2014 06:07 PM, Justin Lemkul wrote: That still doesn't provide anything more useful than before. Please answer the questions I posed in my last message. The essential information is on line 23560 of the problematic topology. -Justin Here is the line: [ angles ] ; aiajak functc0c1 c2c3 2 1 3 5 2 1 4 5 3 1 4 5 (---line 23560) -- 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.
