Thank you Justin and Mark, it worked. I will bare all this in mind.
Akash
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On Behalf Of Justin Lemkul
Sent: 12 April 2019 16:59
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Citrate parameters
On 4/12/19
On 4/12/19 11:57 AM, Pandya, Akash wrote:
How would I find out if there are duplicates or not?
grompp has told you what it is finding as duplicates. You need to look
into the parent force field files and compare the values you are
supplying vs. what are in the existing force field,
How would I find out if there are duplicates or not?
Akash
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On Behalf Of Mark Abraham
Sent: 12 April 2019 16:47
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Citrate parameters
Hi,
It seems
Hi,
It seems that all/most things before the [moleculetype] definition
duplicates the standard contents of the forcefield, as you can see from the
contents of the itp file and the original warnings you mentioned.
Unfortunately you now have the problem of determining whether all of it is
Sorry but I don't quite understand where the duplicates come from? I've pasted
my itp file below:
[ defaults ]
1 2 yes 1.0 1.0
[ atomtypes ]
OC 8 15. -0.760 A 0.302906 0.50208
CC 6 12.0110 0.620 A 0.356359 0.29288
HA 1 1.0080 0.090 A 0.235197 0.09205
CT2 6 12.0110 -0.180 A 0.387541
On 4/12/19 10:52 AM, Pandya, Akash wrote:
Hi all,
My simulation contains citrate molecules. When I try to solvate the system, I
get this error. Can anybody help with this?
Your citrate topology is introducing duplicate parameters that already
exist in the force field. In this instance,
I'm using the CHARMM27 FF and I obtained the parameters from literature.
Akash
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On Behalf Of Soham Sarkar
Sent: 12 April 2019 16:05
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Citrate parameters
Which
Which force field you are using and how you made the itp of the citrate
molecule?
On Fri, 12 Apr 2019, 8:23 pm Pandya, Akash,
wrote:
> Hi all,
>
> My simulation contains citrate molecules. When I try to solvate the
> system, I get this error. Can anybody help with this?
>
> WARNING 1 [file
Hi all,
My simulation contains citrate molecules. When I try to solvate the system, I
get this error. Can anybody help with this?
WARNING 1 [file CITff.itp, line 3]:
Overriding atomtype OC
WARNING 2 [file CITff.itp, line 4]:
Overriding atomtype CC
WARNING 3 [file CITff.itp, line 5]:
Thank you Justin.
Using energy groups is not really that bad.
By using gmx select ‘atomname Cx and resname ADSORBATE and within 0.5 of
resname SURFACE’ -on near.ndx
I can find the atom/s of the adsorbate that is proximal to the surface and
can track the LJ pot’l by frame and use VMD
Hi,
Thanks Mark. See https://redmine.gromacs.org/issues/2924.
Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46
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