Re: [gmx-users] Forcefield parameters for AcetylCoA

2012-07-11 Thread Justin A. Lemkul
Please keep the discussion on the gmx-users mailing list. On 7/11/12 10:43 AM, panbazha wrote: Dear Justin, That file was generated by me in ATB, The issue is when i looked into the united atom itp file, I found many bonds and angles has not determined. So, just wondering if there are any publi

Re: [gmx-users] Forcefield parameters for AcetylCoA

2012-07-11 Thread Justin A. Lemkul
On 7/11/12 8:18 AM, Padmanabhan Anbazhagan wrote: Dear All, Could anyone please suggest me some article or information that contains force field parameters (gromacs53A6) for acetyl Coenzyme A Google turned up: http://compbio.biosci.uq.edu.au/atb/download.py?molid=5470 -Justin -- =

Re: [gmx-users] Forcefield parameters

2010-10-27 Thread Mark Abraham
rote: I think manual 5.3.3 covers the relevant points. Let me know what is not clear. Mark - Original Message - From: Sai Pooja mailto:saipo...@gmail.com>> Date: Wednesday, October 27, 2010 9:41 Subject: Re: [gmx-users] Forcefield parameters

Re: [gmx-users] Forcefield parameters

2010-10-26 Thread Mark Abraham
I think manual 5.3.3 covers the relevant points. Let me know what is not clear. Mark - Original Message - From: Sai Pooja Date: Wednesday, October 27, 2010 9:41 Subject: Re: [gmx-users] Forcefield parameters To: Discussion list for GROMACS users > > > On Tue, Oct 26, 201

Re: [gmx-users] Forcefield parameters

2010-10-26 Thread Sai Pooja
On Tue, Oct 26, 2010 at 6:04 PM, Mark Abraham wrote: > > > - Original Message - > From: Sai Pooja > Date: Wednesday, October 27, 2010 8:52 > Subject: Re: [gmx-users] Forcefield parameters > To: Discussion list for GROMACS users > > > On Tue, Oct 26, 201

Re: [gmx-users] Forcefield parameters

2010-10-26 Thread Mark Abraham
- Original Message - From: Sai Pooja Date: Wednesday, October 27, 2010 8:52 Subject: Re: [gmx-users] Forcefield parameters To: Discussion list for GROMACS users > On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul wrote: > > > Sai Pooja wrote: > > > On T

Re: [gmx-users] Forcefield parameters

2010-10-26 Thread Justin A. Lemkul
Sai Pooja wrote: On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul > wrote: Sai Pooja wrote: On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul mailto:jalem...@vt.edu> >> wrote:

Re: [gmx-users] Forcefield parameters

2010-10-26 Thread Sai Pooja
On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul wrote: > > > Sai Pooja wrote: > > >> >> On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Sai Pooja wrote: >> >>Hi, >> I want to change the non-bonded parameters to modify the >>int

Re: [gmx-users] Forcefield parameters

2010-10-26 Thread Justin A. Lemkul
Sai Pooja wrote: On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul > wrote: Sai Pooja wrote: Hi, I want to change the non-bonded parameters to modify the interaction between water molecules and protein molecules. I am using CH

Re: [gmx-users] Forcefield parameters

2010-10-26 Thread Sai Pooja
On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul wrote: > > > Sai Pooja wrote: > >> Hi, >> I want to change the non-bonded parameters to modify the interaction >> between water molecules and protein molecules. >> I am using CHARMM forcefield with Tip3p water. >> The ffnonbonded.itp file of th

Re: [gmx-users] Forcefield parameters

2010-10-26 Thread Justin A. Lemkul
Sai Pooja wrote: Hi, I want to change the non-bonded parameters to modify the interaction between water molecules and protein molecules. I am using CHARMM forcefield with Tip3p water. The ffnonbonded.itp file of the forcefield has non-bonded parameters for tip3p water. Can I achieve the