Thanks very much for the help. I will see what I can do about that. Sincerely ELie
> Date: Sat, 8 Sep 2012 16:50:00 -0400 > From: [email protected] > To: [email protected] > Subject: Re: [gmx-users] error in producing top file for a structure > > > > On 9/8/12 4:46 PM, Elie M wrote: > > > > > > Thanks a lot for your response. Actually i do have LIG , which obviosuly the > > code did not understand and changed it into LI; at first I thought LI was > > LIG > > but in GROMACS' language. Is there any place where I can read how to > > implement changes in the .rtp file? or any other way to get the correct pdb > > format. i used openbabel because Markin SKETCH and ArgusLAB do not seem to > > keep the charged Nitrogen and Chlorine ions I have got in my structure. By > > the way, I have attached the pdb input file (I guess).. > > > > The list does not accept attachments. If Gromacs is interpreting "LIG" as > "LI" > then the .pdb file is formatted incorrectly - at least one column is shifted, > which will lead to misinterpretation of all of the contents. If you want to > add > a new residue in the .rtp file, refer to the manual, section 5.6.1, in > conjunction with implementation details at: > > 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
