Dear Rui Rodrigues,
That is right. "resid" gives the same residue numbers as those in .gro file.
Thank you very much, also many thanks to Justin, Jianguo, Mark, ...
Jiangfeng.
Jiangfeng Du, PhD Student
Cardiovascular Research Institute Maastricht
Department of Biochemistry
P.O. Box 616
Mobile: +31-681741859
FAX: +31-43-3884159
6200 MD Maastricht
The Netherlands
________________________________________
From: [email protected] [[email protected]] On Behalf
Of [email protected] [[email protected]]
Sent: Friday, February 03, 2012 2:25 PM
To: [email protected]
Subject: gmx-users Digest, Vol 94, Issue 27
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Today's Topics:
1. [Fwd: Re: [gmx-users] problems with KALP-15 IN DPPC
tutorial] ([email protected])
2. Orders of the residues in gromacs
(Joaquim Rui de Castro Rodrigues)
3. Orders of the residues in gromacs (Mark Abraham)
4. trjconv select group (francesca vitalini)
5. Re: topolbuild and charges (Bruce D. Ray)
6. Re: trjconv select group (Justin A. Lemkul)
7. Re: trjconv select group (Mark Abraham)
----------------------------------------------------------------------
Message: 1
Date: Fri, 3 Feb 2012 12:12:30 +0100 (CET)
From: [email protected]
Subject: [Fwd: Re: [gmx-users] problems with KALP-15 IN DPPC
tutorial]
To: [email protected]
Message-ID:
<[email protected]>
Content-Type: text/plain;charset=iso-8859-1
I accomplished the steps related to the removal of the periodicity by my
patch of membrane and to the extension in order to build a bigger bilayer.
The resultant structure appears good..
Now, I'm wondering how to define my box which will be used to perform the
solvatation step. I am new in GROMACS (version 4.0.7) and I need to carry
on the dynamics simulation of the phospholipase protein when this latter
leans on the surface of the membrane (so the protein is not embedded into
the membrane but just leant on that). So far, as I mentioned above, i made
the extension of my dppc128 patch of membrane (I have used nbox parameters
4 4 1).At this point, Have you got any idea about the parameters
necessary to build the box and to do the solvatation? Shall I to consider
even my protein during these steps?How?
Any suggestion will be appreciated,
Silvia
------------------------------
Message: 2
Date: Fri, 3 Feb 2012 11:28:15 +0000
From: Joaquim Rui de Castro Rodrigues <[email protected]>
Subject: [gmx-users] Orders of the residues in gromacs
To: Discussion list for GROMACS users <[email protected]>
Message-ID:
<[email protected]>
Content-Type: text/plain; charset="us-ascii"
Hi,
You are probably mixing "resid" and "residue". In VMD,
- "resid" is taken as found in the file (pdb, gro, etc). You may have several
residues with the same "resid" if you load a file with multiple chains.
- "residue" is generated internally by VMD, it is incremented by one unit for
each residue, even if there are gaps in the sequence, it always starts at 0 and
is granted to be unique for each residue.
Cheers,
Rui Rodrigues
________________________________________
De: [email protected] [[email protected]] Em Nome De Du
Jiangfeng (BIOCH) [[email protected]]
Enviado: sexta-feira, 3 de Fevereiro de 2012 9:06
Para: [email protected]
Assunto: [gmx-users] RE: gmx-users Digest, Vol 94, Issue 24
Dear All,
I found a strange thing about VMD. When I use mouse label residue from graph
(Mouse --> Label --> Atom), i would get a correct residue as it is in .gro
file, while when I use graphics --> representations --> selections, then the
residue selected here is totally different with the one which has the same
number in the .gro file.
Be careful with it, everybody.
Jiangfeng.
Jiangfeng Du, PhD Student
Cardiovascular Research Institute Maastricht
Department of Biochemistry
P.O. Box 616
Mobile: +31-681741859
FAX: +31-43-3884159
6200 MD Maastricht
The Netherlands
________________________________________
Dear Friends,
I want to measure some data of a special residue, for instance TRP143, from my
MD result. But i encountered a problem.
The residue number 143 is ordered in .gro file, while it seems the residue
orders is random in gromacs. It points to another residue when I specify
residue number 143 in VMD or when I am using make_ndx program ( --> r 143; q).
Apparently, gromacs numbering system is not based on the orders in the .gro
structure file.
Does anybody know how to link the gromacs order to the structure file's order
correctly?
Thank you in advance,
Jiangfeng.
Jiangfeng Du, PhD Student
Cardiovascular Research Institute Maastricht
Department of Biochemistry
P.O. Box 616
Mobile: +31-681741859
FAX: +31-43-3884159
6200 MD Maastricht
The Netherlands
------------------------------
Message: 4
Date: Thu, 02 Feb 2012 12:43:17 -0500
From: "Justin A. Lemkul" <[email protected]>
Subject: Re: [gmx-users] Orders of the residues in gromacs
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Du Jiangfeng (BIOCH) wrote:
> Dear Friends,
>
> I want to measure some data of a special residue, for instance TRP143, from
> my MD result. But i encountered a problem.
>
> The residue number 143 is ordered in .gro file, while it seems the residue
> orders is random in gromacs. It points to another residue when I specify
> residue number 143 in VMD or when I am using make_ndx program ( --> r 143;
> q). Apparently, gromacs numbering system is not based on the orders in the
> .gro structure file.
>
> Does anybody know how to link the gromacs order to the structure file's order
> correctly?
>
Depending on the Gromacs version you're using, residue numbering is treated
differently. In pdb2gmx, you can choose to renumber the residues from 1 or not.
The default is to not renumber the file. You should check to see what you did
with respect to this option and whether or not your coordinate file is numbered
from 1. If it is not, then what you think is residue 143 may not be interpreted
that way by all external programs, depending on whether or not they respect the
numbering of the .gro file.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 8
Date: Fri, 3 Feb 2012 10:04:28 +0800 (SGT)
From: Jianguo Li <[email protected]>
Subject: Re: [gmx-users] Orders of the residues in gromacs
To: Discussion list for GROMACS users <[email protected]>
Message-ID:
<[email protected]>
Content-Type: text/plain; charset="iso-8859-1"
Another possible reason is due to vmd, which numbers the residue from 0.
Residue 143 in gromacs corresponds to residue 142 in vmd.
Cheers,
Jianguo
________________________________
------------------------------
Message: 3
Date: Fri, 03 Feb 2012 23:40:23 +1100
From: Mark Abraham <[email protected]>
Subject: [gmx-users] Orders of the residues in gromacs
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 3/02/2012 7:26 PM, Du Jiangfeng (BIOCH) wrote:
> Dear Justin and Jiangguo,
>
> It's still the issue about residue numbering. Actually, the gromacs version
> is 4.5.3, and I am using Martini coarse grained simulation, where I presume
> that gromacs reads residues from .gro file randomly, because there are no
> residues fetched correctly when I picked a list of residues for testing.
>
> Plus, I didn't use pdb2gmx program. In my gro file, it contains protein,
> lipids, ion, and water.
>
> :( :( :( :( :( :(
Residue numbering is not random - there's a rule that you don't
understand, and that's quite a different thing :-) If you are interested
in learning how to manage the rule, then there are better ways to
approach your search for knowledge than to suggest that people providing
you with free tools have gone out of their way to make their use
frustrating! :-)
Mark
------------------------------
Message: 4
Date: Fri, 3 Feb 2012 14:21:37 +0100
From: francesca vitalini <[email protected]>
Subject: [gmx-users] trjconv select group
To: [email protected]
Message-ID:
<CAPRCF+K3HJdbnCs-VdYP3kuSyXF2ODf6xOvv8p7QHbp05y=v...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi!
I have to use the gromacs command trjconv to obtain a .gro file from a .xtc
and a .pdb file. I have to do it for several files in a bash for loop so
I'd rather prefer to find a way to make my script type in the trjconv
interactive terminal always the same number for the system. Any tips?
Thanks
Francesca
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Message: 5
Date: Fri, 3 Feb 2012 05:23:13 -0800 (PST)
From: "Bruce D. Ray" <[email protected]>
Subject: Re: [gmx-users] topolbuild and charges
To: Discussion list for GROMACS users <[email protected]>
Message-ID:
<[email protected]>
Content-Type: text/plain; charset="iso-8859-1"
On Friday, February 3, 2012 at 12:31 AM, Tom <[email protected]> wrote:
?
> Any one has the experience of topolbuild?
>
> I tried to build *top file with the software of topolbuild
>?
>? ./topolbuild -n lipid -dir
>/home/computer/Tom/topbuild/topolbuild1_3/topolbuild1_3/dat/gromacs -ff oplsaa
>?
> I chose oplssaa. But from the generated *top file,these charges in *top file
> can
> not match the partial charges in file (in gromacs package)?of
> /opt/gromacs-4.5.4/share/gromacs/top/oplsaa.ff/ffnonbonded.itp
>?
> How to understand these charges on *top file, which topolbuild generates?
> Thanks for your instruction!
?
First, topolbuild never "generates" charges.? Unless the -charge option is
specified,
the charges come from whatever is read as being the charge entry in the *.mol2
file.
If the charge type in the header of the *.mol2 file reads "INVALID", or
"NO_CHARGE",
the charges are reset to 0 as the *.mol2 file is read.? If the -charge option
is given,
topolbuild assigns charges given in the "Atoms data" section of the force field
parameters file in the directory pointed to by the -dir entry according to
assigned
atom type.? In the case of oplsaa, the parameters file is ffoplsaa.dat, the
column is
labeled charge, and the assignment is based on oplsaa atom type number.? All of
this, of course, relies on the *.mol2 file being syntactically correct
according to
the rules given by Tripos, Inc.? Some programs that attempt to write *.mol2
files
fail to write complete Sybyl atom types.? Others do write complete atom types,
but sometimes have problems getting the atom type correct, most notably with
the guanidino carbon of arginine which is supposed to be C.cat
I hope this short note helps.
?
--
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
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------------------------------
Message: 6
Date: Fri, 03 Feb 2012 08:23:25 -0500
From: "Justin A. Lemkul" <[email protected]>
Subject: Re: [gmx-users] trjconv select group
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
francesca vitalini wrote:
> Hi!
> I have to use the gromacs command trjconv to obtain a .gro file from a
> .xtc and a .pdb file. I have to do it for several files in a bash for
> loop so I'd rather prefer to find a way to make my script type in the
> trjconv interactive terminal always the same number for the system. Any
> tips?
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 7
Date: Sat, 04 Feb 2012 00:25:03 +1100
From: Mark Abraham <[email protected]>
Subject: Re: [gmx-users] trjconv select group
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 4/02/2012 12:21 AM, francesca vitalini wrote:
> Hi!
> I have to use the gromacs command trjconv to obtain a .gro file from a
> .xtc and a .pdb file. I have to do it for several files in a bash for
> loop so I'd rather prefer to find a way to make my script type in the
> trjconv interactive terminal always the same number for the system.
> Any tips?
Check out
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
Mark
------------------------------
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