[gmx-users] RE: gmx-users Digest, Vol 94, Issue 27
Du Jiangfeng (BIOCH)
j.du at maastrichtuniversity.nl
Fri Feb 3 15:25:03 CET 2012
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: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of gmx-users-request at gromacs.org [gmx-users-request at gromacs.org]
Sent: Friday, February 03, 2012 2:25 PM
To: gmx-users at gromacs.org
Subject: gmx-users Digest, Vol 94, Issue 27
Send gmx-users mailing list submissions to
gmx-users at gromacs.org
To subscribe or unsubscribe via the World Wide Web, visit
http://lists.gromacs.org/mailman/listinfo/gmx-users
or, via email, send a message with subject or body 'help' to
gmx-users-request at gromacs.org
You can reach the person managing the list at
gmx-users-owner at gromacs.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."
Today's Topics:
1. [Fwd: Re: [gmx-users] problems with KALP-15 IN DPPC
tutorial] (scaprari at uniroma3.it)
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: scaprari at uniroma3.it
Subject: [Fwd: Re: [gmx-users] problems with KALP-15 IN DPPC
tutorial]
To: gmx-users at gromacs.org
Message-ID:
<28536.193.205.142.131.1328267550.squirrel at mail.uniroma3.it>
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 <joaquim.rodrigues at ipleiria.pt>
Subject: [gmx-users] Orders of the residues in gromacs
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<2B249782AAD08A40B261ACD7AFF480B6034E5151E974 at mbx01.IPLeiria.pt>
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: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] Em Nome De Du Jiangfeng (BIOCH) [j.du at maastrichtuniversity.nl]
Enviado: sexta-feira, 3 de Fevereiro de 2012 9:06
Para: gmx-users at gromacs.org
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" <jalemkul at vt.edu>
Subject: Re: [gmx-users] Orders of the residues in gromacs
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4F2ACB35.8050808 at vt.edu>
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 <ljggmx at yahoo.com.sg>
Subject: Re: [gmx-users] Orders of the residues in gromacs
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<1328234668.1600.YahooMailNeo at web190204.mail.sg3.yahoo.com>
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 <Mark.Abraham at anu.edu.au>
Subject: [gmx-users] Orders of the residues in gromacs
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4F2BD5B7.1050207 at anu.edu.au>
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 <francesca.vitalini11 at gmail.com>
Subject: [gmx-users] trjconv select group
To: gmx-users at gromacs.org
Message-ID:
<CAPRCF+K3HJdbnCs-VdYP3kuSyXF2ODf6xOvv8p7QHbp05y=VcA at 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120203/da5eaaa8/attachment-0001.html
------------------------------
Message: 5
Date: Fri, 3 Feb 2012 05:23:13 -0800 (PST)
From: "Bruce D. Ray" <brucedray at yahoo.com>
Subject: Re: [gmx-users] topolbuild and charges
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<1328275393.96069.YahooMailNeo at web126102.mail.ne1.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"
On Friday, February 3, 2012 at 12:31 AM, Tom <dnaafm at gmail.com> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120203/15c36823/attachment-0001.html
------------------------------
Message: 6
Date: Fri, 03 Feb 2012 08:23:25 -0500
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] trjconv select group
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4F2BDFCD.5060300 at vt.edu>
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 <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] trjconv select group
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4F2BE02F.4030002 at anu.edu.au>
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
------------------------------
--
gmx-users mailing list
gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
End of gmx-users Digest, Vol 94, Issue 27
*****************************************
More information about the gromacs.org_gmx-users
mailing list