Dear all,
Is the form of the .n2t file (read by x2top to produce the top file) the same
for all forcefields? I am using the CHARMM forcefield but I could not find an
ffcharmm27.n2t file.
Regards
Elie --
gmx-users mailing listgmx-users@gromacs.org
forcefield
On 10/10/12 10:35 PM, Elie M wrote:
Dear all,
Is the form of the .n2t file (read by x2top to produce the top file) the
same for all forcefields? I am using the CHARMM forcefield but I could not
find an ffcharmm27.n2t file.
The .n2t format is universal. Most force
] .n2t file for the CHARMM forcefield
On 10/10/12 11:11 PM, Elie M wrote:
Ok. This means that I have to form the .n2t file for the CHARMM field as it
is required by x2top. For the OPLSAA field the format was:
Copls_1570.000 12.011 4H 0.108 H 0.108 H 0.108 C
Dear all,
Does anyone know where I can find reference of how to calculate the RB
parameters (C0-C5) for proper dihedrals? I have got some undefined dihedrals in
my top file and I am not sure where to start. What kind of information do i
need to calculate those parameters? any package that does
to Hydrogen because the symbol
is SH?? maybe this is the source of the error and I have to redefine things in
the .n2t file?
Elie
Date: Fri, 5 Oct 2012 13:06:34 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/5/12 1:00 PM, Elie M
: Re: [gmx-users] Error with grompp
On 10/6/12 1:18 PM, Elie M wrote:
This is what I did. For example one of the [bonds] problems is a bond
between S and one of the carbons C in the thiophene molecule. In the n2t
file. I have added OPLSA_734 S because it si related to all-atom S
it is a
bit weird because the bond is there in the file then why it cannot find it? Any
suggestions?
Elie
Date: Sat, 6 Oct 2012 13:59:10 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/6/12 1:57 PM, Elie M wrote:
Yes I just
On 10/4/12 5:56 PM, Elie M wrote:
I guess the first parameter of each pair is easy to find. what about kb? k
theta?. kb is the force constant isnt it? any reference about a method
how to calculate them please? pr anything atht might be of help.
Bonded parameters
On 10/3/12 7:48 PM, Elie M wrote:
Sorry it seems that those breaks are due to hotmail and not present in the
topology. Thanks for your reply. I still have problems...I will tell u
briefly and as clear as possible what i did.
(1) My top file has the following lines ate first
the source of error be known and corrected?
Elie
Date: Thu, 4 Oct 2012 10:26:04 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/4/12 10:12 AM, Elie M wrote:
Hello everyone,
Justin, I have repeated the procedures without doing any
Oct 2012 12:25:48 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/4/12 12:13 PM, Elie M wrote:
Thanks a lot. I have sorted out the error that occured in the
ffoplsaabon.itp; I have commented ; one line which was given the first
-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/4/12 4:22 PM, Elie M wrote:
I guess now I get what is happening finally. Correct me if I am wrong. The
.top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which
was also modified to include atoms
-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Elie M
Sent: Tuesday, 2 October 2012 1:39 PM
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Error with grompp
I am a bit confused..I am getting different errors though similar in goal.
The error
@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/3/12 10:03 AM, Elie M wrote:
Hello Emanuel.
First of all thank you for your help. I am sorry if my previous e-mail was
a bit confusing. I will tell what I did recently.
(1) I removed all the information :molecule type
Thanks for your time and help as always. I will see what I can do about that.
Elie
Date: Mon, 1 Oct 2012 08:38:15 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/1/12 12:38 AM, Elie M wrote:
Dear all,
Maybe this error has
to match that .top
file or what? and which file should be in the same order of which?
Thanks
Elie
Date: Mon, 1 Oct 2012 08:38:15 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/1/12 12:38 AM, Elie M wrote:
Dear all,
Maybe
Dear all,
Maybe this error has been discussed before; I have checked previous messages on
it but i could not resolve it. I have done a modified version of the oplsaa
forcefield which I have called ffoplsaamod.n2t. The top file was created
successfully. However when I run grompp, I get the
Dear all,
I am trying to minimize the energy of a polymer system I have. I have
successfully modified the n2t file to include force fields for atoms that were
not present. However now I am using grompp before using mdrun (to minimize).
However I have a question should the .ITP and .RTP files
Dear all,
i am trying to convert a .gro file into a top file using .x2top but not all
atoms can be assigned forcefields and the code stops with the error:
Generating bonds from distances...atom 94Can not find forcefield for atom C-2
with 2 bondsCan not find forcefield for atom S-3 with 0
] error with x2top.
On 9/25/12 4:28 PM, Elie M wrote:
Dear all,
i am trying to convert a .gro file into a top file using .x2top but not all
atoms can be assigned forcefields and the code stops with the error:
Generating bonds from distances...atom 94Can not find forcefield for atom
C
Yep You are right. I will try my best to change the files accordingly.
Thanks
Date: Tue, 25 Sep 2012 17:05:20 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] error with x2top.
On 9/25/12 5:02 PM, Elie M wrote:
Thanks for your reply. I guess either
.
On 9/25/12 5:02 PM, Elie M wrote:
Thanks for your reply. I guess either way (x2top or pdb2gmx), I have
problems. pdb2gmx is giving the same old error residue 'UNK' is not
found in topology residue file whereas strangely enough x2top did not
complain and was able to assign
Dear all,
I have created a .GRO file from a PDB file for a polymer. However in the PDB I
have positive and negative charges of some ions where as in the produced GRO
file these disappear. Are those charged atoms taken into account in the gro
file as I will be doing a MD simulation of such
Thanks for your help.
Elie
Date: Mon, 24 Sep 2012 13:05:14 +0800
Subject: Re: [gmx-users] Missing charges in a .gro file
From: terrence...@gmail.com
To: gmx-users@gromacs.org
On Mon, Sep 24, 2012 at 12:56 PM, Elie M elie.mouj...@hotmail.co.uk wrote:
Dear all,
I have created
Dear all,
I am trying to use editconf to produce a .GRO file from an .XYZ file but I am
getting the following error:
Program editconf, VERSION 4.0.5Source code file: futil.c, line: 330
File input/output error:S54NONSOLV.xyz.gro
Some of the input file is:46S54 NONSOLVATED POLYMERC 5.33751
Date: Wed, 19 Sep 2012 05:23:28 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] use of PRODRG
On 9/18/12 10:35 PM, Elie M wrote:
Dear all,
I have been reading about PRODRG that takes a PDB file as an input and
produces topologies compatible
Thanks for your time and help as usual.
Elie
Date: Wed, 19 Sep 2012 13:47:26 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] use of PRODRG
On 9/19/12 11:40 AM, Elie M wrote:
I don't understand this. PRODRG will be of no use here since you are using
Dear all,
I have been reading about PRODRG that takes a PDB file as an input and produces
topologies compatible with GROMACS as an output. Can this program be then
considered as a solution to the problem of missing residues in GROMACS like
LIG?
N.B: I am using the OPLSAA force field .I also
dumped error)
On 9/14/12 12:19 AM, Elie M wrote:
Dear all, I am trying to study the MD of a Carbon Nanotube interacting with
some polymers. and I have some problems in forming the topology files. I
have actually two questions and I hope you can help me in that.
(1) In an attempt
Dear all,
I have a small question regarding energy minimization. I am minimizing a carbon
naotube in vaccuo and my (mdp )input file is: ;
; SWNT (10,0) on its own
; Elie Moujaes, SWNT+polymers project
; Energy minimization input file
;
cpp =/usr/bin/cpp
define
Thank you for your reply and help.
Regards
Elie
Date: Sat, 15 Sep 2012 13:32:06 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] energy minimisation of carbon nanotubes.
On 9/15/12 12:49 PM, Elie M wrote:
Dear all,
I have a small question regarding
Dear all, I am trying to study the MD of a Carbon Nanotube interacting with
some polymers. and I have some problems in forming the topology files. I have
actually two questions and I hope you can help me in that.
(1) In an attempt to form the topology files of CNTs and graphene (using
x2top),
Dear all,
I am new to GROMACS. I am trying to minimize a structure but first I have to
form the pdb file with the correct force field parameters. I am using version
4.0.5 and an OPLSAA force field. The error I am getting is:...Opening
library file
...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] error in producing top file for a structure
On 9/8/12 4:29 PM, Elie M wrote:
Dear all,
I am new to GROMACS. I am trying to minimize a structure but first I have
to form the pdb file with the correct force field parameters. I
Thanks very much for the help. I will see what I can do about that.
Sincerely
ELie
Date: Sat, 8 Sep 2012 16:50:00 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] error in producing top file for a structure
On 9/8/12 4:46 PM, Elie M wrote:
Thanks
35 matches
Mail list logo
