...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, August 29, 2011 3:06 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] amber DNA non-integer charge
Kamesh Narasimhan wrote:
> I am using Gromacs 4.0.5 and in my ffamber03.rtp I can see that the charges
> are
t
0.3055
31 amber99_44 1DG5O3' 31-0.5232 16 ; qtot
-0.2177
.
...
.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, August 29, 2011 2:41 AM
To: Discussion list for GROMA
_
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, August 29, 2011 2:41 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] amber DNA non-integer charge
Kamesh Narasimha
Kamesh Narasimhan wrote:
Hil,
I am trying to simulate a protein-DNA structure using amber03 and end up having
a non-integer charge in topology generation . From the webpage of ffamber on
NA-simulations, I could see this below instruction
"However, for nucleic acids this also often causes p
Hil,
I am trying to simulate a protein-DNA structure using amber03 and end up having
a non-integer charge in topology generation . From the webpage of ffamber on
NA-simulations, I could see this below instruction
"However, for nucleic acids this also often causes pdb2gmx to replace an H atom
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