Hello,
I am trying to run a GROMACS simulation with few amino acids covalently bound
to Palmitoyl-linoleylphosphatidylcholine molecules., by using GROMOS ff. I
found the lipid structure and parameters on Tieleman`s website, but I don`t
know how to get the parameters for covalently bound
Yes the error message indicates about the line which is in the very end ( 6 7
2 gb_27). I can see which atoms they are, 6 and 7, but I don`t know how to
solve it??? My part of top file is below, with the line it is complaining about
in bold. Thank you very much.
Include forcefield
7:15 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] free energy calculations for reference state for
constant pH MD simulations...
On 1/30/14, 2:27 PM, Ozbil, Mehmet wrote:
For Dummy atom, I tried to write DUM for atom type and give 0 charge but it
could not recognize
during deprotonation).
On Wed, Jan 29, 2014 at 8:15 PM, Ozbil, Mehmet m.oz...@umiami.edu wrote:
Thanks Bipin for the reply.
I went through the Gromacs manual, and thought that I managed to
incorporate two states (protonated and deprotonated) in my topology file.
Can anyone who has done
a dummy atom, but the C
and both O atoms of the resulting COO- group will be different depending on
protonation state. See GLU/GLUH in aminoacids.rtp.
-Justin
On Thu, Jan 30, 2014 at 8:55 PM, Ozbil, Mehmet m.oz...@umiami.edu wrote:
I see Bipin,
Thanks. One quick question though, am I going
are affected by the removal of the proton. Only H becomes a dummy atom,
but the C and both O atoms of the resulting COO- group will be different
depending on protonation state. See GLU/GLUH in aminoacids.rtp.
-Justin
On Thu, Jan 30, 2014 at 8:55 PM, Ozbil, Mehmet m.oz...@umiami.edu
wrote
a dummy atom,
but the C and both O atoms of the resulting COO- group will be different
depending on protonation state. See GLU/GLUH in aminoacids.rtp.
-Justin
On Thu, Jan 30, 2014 at 8:55 PM, Ozbil, Mehmet m.oz...@umiami.edu
wrote:
I see Bipin,
Thanks. One quick question though, am I
-boun...@maillist.sys.kth.se on behalf of Justin Lemkul
jalem...@vt.edu
Sent: Thursday, January 30, 2014 1:43 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] free energy calculations for reference state for
constant pH MD simulations...
On 1/30/14, 1:39 PM, Ozbil, Mehmet wrote
for
constant pH MD simulations...
See the section 5.7.4 Topologies for free energy calculations in Gromacs
4.6.5 manual.
On Tue, Jan 28, 2014 at 3:09 AM, Ozbil, Mehmet m.oz...@umiami.edu wrote:
Hello,
I am trying to run constant pH MD with GROMACS, and started with the TI
free energy
