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
