Re: Topology file for ethanol

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
and NAMD.

Please advise.

Best
Babban

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:
> http://mackerell.umaryland.edu/CHARMM_ff_params.html#CGenFF
>
> Good luck.
>
> --Farid
> ------------------------------
> *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
> ?*
>
> Thanks!
>

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