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)..
Thanks once again Elie > Date: Sat, 8 Sep 2012 16:37:16 -0400 > From: [email protected] > To: [email protected] > Subject: Re: [gmx-users] error in producing top file for a structure > > > > On 9/8/12 4:29 PM, Elie M wrote: > > > > Dear all, > > I am new to GROMACS. I am trying to minimize a structure but first I have > > to form the pdb file with the correct force field parameters. I am using > > version 4.0.5 and an OPLSAA force field. The error I am getting > > is:.......Opening library file > > /cygdrive/c/Packages/Gromacs/share/gromacs/top/ffOPLSAA-c.tdbProcessing > > chain 1 (46 atoms, 1 residues)There are 4 donors and 2 acceptorsThere are 0 > > hydrogen bonds > > -------------------------------------------------------Program pdb2gmx, > > VERSION 4.0.5Source code file: pdb2gmx.c, line: 429 > > Fatal error:Atom C in residue LI 1 not found in rtp entry with 1 atoms > > while sorting > > atoms------------------------------------------------------- > > I read about the error but i could not figure out the "mismatch" that was > > stated in the input file which you will find attached. Please can anyone > > help me > > The error comes from the fact that pdb2gmx is finding a carbon atom in a > residue > named LI (which is lithium). Of course, that is nonsense. Without seeing > the > .pdb file, it's hard to say what's going on, but if you have some residue > named > "LIG" (which will also be unknown to pdb2gmx) then perhaps the format of the > .pdb file is wrong. That's just a wild guess though. But of course, if you > have "LIG" then you will need to add all the necessary parameters to the .rtp > file anyway. > > -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
