[gmx-users] simple question about rtp and pdb file
Justin A. Lemkul
jalemkul at vt.edu
Mon May 3 02:22:45 CEST 2010
> Dear Justin,
> Thank you so much for your help. Could you please help me with some
> simple questions:
> 1- Regarding the atom types: For n-Hexane why did not you choose atom types:
> opls_068 15.03500 ; CH3 (C2) N-ALKANES
> opls_071 14.02700 ; CH2 (SP3) ALKANES
> rather than:
> opls_157 12.01100 ; all-atom C: CH3 & CH2, alcohols
> opls_158 12.01100 ; all-atom C: CH, alcohols
> I would like to know the reason because I am confused which type to pick up.
; Types 1-134 are from the united-atom OPLS, which can be
; useful for solvents and/or CH2 optimizations (e.g. in lipids).
; Explicit all-atom parameters start with opls_135.
I assumed you were using OPLS-AA, rather than the (very old) OPLS-UA.
> 2-Please tell me what the difference between atom type C and CA is?
There are no atom types named C or CA. Are you referring to atom names in the
.pdb file? The atom names are unimportant, and were generated automatically by
> 3- Regarding pdb file:
> 3-1-How did you create this pdb file?
> 3-2- Why HETATM rather than ATOM?
That's just what PRODRG produces. It's not important.
> I searched for HETATM and ATOM and I found this:
> ATOM:Atomics coordinate records for standard groups
> HETATM: Atomics coordinate records for heterogens
> What does this mean?
Normally PDB files have some biological macromolecule (protein or DNA, etc) and
ligands are listed as HETATM. For use in Gromacs, this is an irrelevant
> 4-In my Pdb file I had zero numbers for the last two columns. What is
> the reason for 1 and 20 figures in this pdb file?
That's just what PRODRG does. For structures that were not derived
experimentally, these fields are irrelevant.
> 5-and finally, do I need to add the rtp file to ffoplsaa.rtp in
> share/gromacs/top directory?
No. You can make a local copy of the file in your working directory, and it
will be read first by pdb2gmx. This is generally preferable so you are not
altering a file system-wide, especially if you accidentally mess something up :)
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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