[gmx-users] simple question about rtp and pdb file

[Justin A. Lemkul]

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

-- 
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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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