Thanks for your replies. I found the residuetypes.dat file in top directory of GROMACS package. I need to add the FOR to this file. But it's question for me where am I supposed to set the residuetypes.dat file? In FF folder existed in my working directory?
Sincerely, Shima ----- Original Message ----- From: Justin A. Lemkul <[email protected]> To: Discussion list for GROMACS users <[email protected]> Cc: Sent: Tuesday, June 26, 2012 8:20 PM Subject: Re: [gmx-users] H-atoms in .hdb file On 6/26/12 11:47 AM, Shima Arasteh wrote: > OK, but when I chose none, it gives me a fatal error ( dangling bond! ). A > new problem! So how do I solve it? > "Dangling bond" errors were introduced as part of the output in Gromacs 4.5. The "aminoacids.dat" file was only used by older (4.0.x and earlier) versions of Gromacs. You need to be modifying "residuetypes.dat" to indicate that FOR is a Protein residue so that the chain is continuous with respect to its content type. http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist 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 list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
