Moeed wrote:
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.
From ffoplsaa.atp:
; 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
PRODRG.
<snip>
3- Regarding pdb file:
3-1-How did you create this pdb file?
PRODRG.
http://davapc1.bioch.dundee.ac.uk/prodrg/
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
distinction.
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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