From: Babban Mia (babbanmia_at_gmail.com)
Date: Wed Aug 10 2011 - 23:35:37 CDT
I can not use two topology file simultaneously like topall27_lipid.inp for
my protein and water(TIP3) and use another cgenff for ethanol.I need to have
everything in one single topology file.
Moreover I guess the cgenff were like the oldest topology and parameter
files and lot of people suggest against using them in new versions of CHARMM
On Thu, Aug 11, 2011 at 9:46 AM, Ismail, Mohd F. <farid_at_ou.edu> wrote:
> I just check cgenff, and they have ethanol in it:
> Good luck.
> *From:* owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of
> Babban Mia [babbanmia_at_gmail.com]
> *Sent:* Wednesday, August 10, 2011 10:58 PM
> *To:* namd-l_at_ks.uiuc.edu
> *Subject:* namd-l: Topology file for ethanol
> Hello Everyone
> As I had mentioned in my last post that I am setting up a solvation box
> having ethanol and water molecules which I created using packmol.
> To be able to use the pdb file of that simulation file which has water in
> TIP3 representation ,ethanol molecules and protein ,I need a single topology
> file which would find representation for all things present in the
> simulation box?
> I am currently using top all27_lipid topology file which has representation
> for my entire protein and water molecules in TIP3 represenation
> *Can somebody please advise me about a topology file which would cater to
> my ethanol molecules as well ?
> Is the TIP3 representation good enough when water is being used as solvent
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