Re: [gmx-users] ATP for

[TJ Piggot]

From the Carlson et al. paper where these ATP parameters were published and 
through choosing the appropriate amber_X atom types from the .atp (and the 
corresponding values for these types in the nb and bon .itp files). As I 
mentioned previously you need to add a new O3 atom type to these files 
based on the information in the Carlson paper.


If you have a look at one of the entries from the ffamberXX.rtp file and 
work out how this is used by pdb2gmx it should become clear what you need 
to do to add the ATP to the forcefield.


Cheers

Tom

--On Saturday, February 06, 2010 00:05:10 +0530 Chandan Choudhury 
iitd...@gmail.com wrote:




Hi Thomas !

Creating a new entry in the .rtp, nb.itp needs charge, radius, epsilon
values etc. values. Where to get these values


Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA



On Fri, Feb 5, 2010 at 6:54 PM, Thomas Piggot t.pig...@bristol.ac.uk
wrote:

Not sure about amb2gmx.pl or acpypi but you can do this by hand. Consult
the GROMACS manual (Chapter 4) for the equations to convert the
parameters into GROMACS format.

I would also say that the easiest way would be to create a new entry in
the .rtp and then also add the appropriate bonded parameters into the
bon.itp file, making sure to include the bonded parameters for the new O3
atom type. Do note that you need to also add this new atom type for the
O3 oxygen into the .atp file and the non-bonded parameters for the atom
type into the nb.itp file.

You can also add entries into the .hdb to allow pdb2gmx to add the
appropriate hydrogens to your ATP if so desired. If not, your input pdb
for pdb2gmx will need to have these hydrogens already included.

Cheers

Tom

Chandan Choudhury wrote:


Hello gmx users,
I need to use ATP's parameter for amber port in gromacs. The atp.prep and
frcmod.phos for ATP can be found at
http://www.pharmacy.manchester.ac.uk/bryce/amber. How can I use it in
ffamber.
 The program amb2gmx.pl http://amb2gmx.pl needs amber to be installed,
which is not present. Same with ACPYPI.


Any suggestion will be very helpful.

Chandan


--
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NCL, Pune
INDIA



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Re: [gmx-users] define a new covalent bond in gromacs

[TJ Piggot]

How about using bond type 6 to restrain the distance without actually 
creating a bond between the atoms?


Tom

--On Tuesday, January 05, 2010 22:57:32 +0100 David van der Spoel 
sp...@xray.bmc.uu.se wrote:



Hans HEINDL wrote:

mdrun-openmm does not yet support any restraints

But gromacs does. Therefore, it seems you need to patch openmm, for which
you probably want to contact the openmm team.


Hans

Am Dienstag, den 05.01.2010, 22:12 +0100 schrieb David van der Spoel:

Hans HEINDL wrote:

Hi all,

I need to restrain the distance of two atoms in my system (the distance
is around 57 angstroms). As we plan to use mdrun-openmm which presently
does not support neither distance nor position restraints we need to
create a new covalent bond between the two atoms which would restrain
the distance of the two atoms. (This was Peter Eastmans idea from
Standford) How could we do that and where would be the best place to
define (I presume the *.top file) the bond and where should the bond
length and spring constant be defined?

Thanks in advance

Hans HEINDL
University of Westminster
London UK


How about normal distance restraints? Have you checked the manual?

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Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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[gmx-users] FWD:simulationg a distance restraint with a type 6 bond in gromacs

[TJ Piggot]

Please keep all correspondence on the GROMACS mailing list, it gives you a 
much greater chance of someone being able to help you.


I have used this bond type before and have had no problems (with force 
constants much smaller than those which you apply). I would make sure that 
your box is big enough so that this bond is not being applied across the 
boundary. Otherwise someone else may have more ideas to help you.


Tom

 Forwarded Message 
Date: Wednesday, January 06, 2010 22:43:20 +0100
From: Hans HEINDL hhei...@terra.es
To: TJ Piggot t.pig...@bristol.ac.uk
Cc:
Subject: simulationg a distance restraint with a type 6 bond in gromacs

Hi,

As you remember we discussed simulation of a restraint which is not yet
implemented in mdrun-openmm by creating a 'bond'. Type 1 bonds did not
work but the type 6 did the job but I could not restrain the distance at
the value I projected. The distance between the ends of my peptide
should remain 57 angstroms and the best I accomplished was holding the
distance fairly well for a ns and then it broke down to a much smaller
value. (I tried to define the bond with:

1   614 65.761 40

with the energy term for the bond length obviously too small. But even
if I got up to 300 000 000 up to 1 000 000 000 I got no proper result.

The best results were recieved with

1   614 5   5.671   5.671   5.671   5.671

but even with such an extreme example the distance tended to shrink


kind regards

Hans HEINDL 
University of Westminster UK



-- End Forwarded Message --



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Re: [gmx-users] get 3 roation angles over time

[TJ Piggot]

You could use g_principal and follow the change in angles of the three 
principal axes of your group using simple maths. This might give you what 
you are looking for.


Another way to look at rotations is to use the program DynDom, but this 
only works on individual structures not trajectories.


Tom

--On Friday, January 01, 2010 10:49:44 +0100 Tsjerk Wassenaar 
tsje...@gmail.com wrote:



Hi Marc,

Which rotation angles? I suppose you mean the Euler angles, but then,
XYZ, XYX, ZYZ? I may be able to help. Contact me off list if you're
interested.

Cheers,

Tsjerk

On Fri, Jan 1, 2010 at 9:02 AM,  marc.spen...@gmx.net wrote:

Dear Gromacs users,

my system consists of two rigid bodies a and b. The body a has no
rotation or translation over time. Body b rotates and translates over
time. For my system I got the initial structure as PDB file and a XTC
trajectory. How do I get in any easy way from the XTC trajectory the
three rotation angles of the rigid body b over time (someting like a 3
column output file) ?

I already searched the gromacs mailinglist and I locked at the commands
g_rms, g_rdf, g_sorient, g_chi, g_confrms, g_bundle and
g_rmsf. But it seems that non of the commands really does what I want
:( .

Any help is welcome, thanks and a happy new year
Marc

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Re: [gmx-users] when using RB dihedral function, how to exclude 1-4 vdw ?

[TJ Piggot]

If you read this part of the manual again you will see that it discusses 
this point of 1-4 interactions for the OPLS forcefield and RB dihedrals 
(and the same as discussed for OPLS is true for the AMBER forcefields using 
RB  potentials for dihedrals).


Tom

--On Friday, November 20, 2009 16:45:44 +0800 XunJie Yang 
yangx...@mail.ustc.edu.cn wrote:



Hello GMX users:
  I'm new to GMX and I'm now facing a problem. For short, it is about how
to properly use the RB function.   I'm now doing simulation with AMBER
force field(ported to GMX by FFAmber), which employs Ryckaert-Bellemans
function for dihedral, it is how FFAmber forcefield treats dihedral
angles as the parameters provided are only for RB function.According
to GMX Manual page 62, using RB function implies exclusion of 1-4 LJ
interactions between the first and last atom of the dihedral, which
means, I should turn off the 1-4 vdw term while retaining the 1-4 coulomb
term. However, I haven't found the way of doing so. If I deleted the
[pairs] block in the topology file, all 1-4 interactions including 1-4
coulomb interaction would be deleted.   Could anyone who knows key to
this problem give me some help? Thanks in advance!

Yang Xunjie
2009-11-20
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RE: [gmx-users] Pushing MD further

[TJ Piggot]

I would also add that you could also use TEE-REX which overcomes some of 
the problems associated with normal REMD on large systems. Do note that as 
far as i know the TEE-REX patch only works with GROMACS versions 3.3.x and 
so each replica in the TEE-REX simulation can only be ran on one CPU, 
meaning that these simulations can take a long time.


Tom

--On Friday, November 20, 2009 16:11:38 +0100 Berk Hess g...@hotmail.com 
wrote:



Hi,

I would think any system with a membrane in it is too large to gain much
with REMD
(unless you are interested in the temperature dependence).

You can use essential dynamics sampling or flooding, see make_edi.

Berk


Date: Fri, 20 Nov 2009 10:00:11 -0500
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Pushing MD further



Thielges, Sabine wrote:
 Hi,

 I am currently running some GPRC MD with membrane. After a lot of trial
 I now have a nice 25 ns run with an agonist. But the final structure is
 too close the starting and I know it is far from what the biology
 describes.
 I would like to know if there is options that I can add to my md.mdp
 file to make the MD explores some other area.


There is no magic .mdp option to make sampling better, and you can not
necessarily ever trust the results of just one single simulation. There
are  several options to enhance sampling:

1. Simulated annealing
2. Replica-exchange MD
3. Additional simulations with different starting velocities

With #2, bilayers can be quite problematic. A recent paper from Max
Berkowitz's  group in JPCB has a nice protocol for REMD with a membrane.

-Justin

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Virginia Tech
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Re: [gmx-users] Urea Topology

[TJ Piggot]

They are published in the paper by smith et al. (J. Phys. Chem. B 2004, 
108, 1065-1071) and have also been posted previously on this mailing list 
(both of which can be found through a simple search). Please note that the 
parameters posted on the mailing list are not quite correct as they have 
they have the force constant for the impropers in kJ/mol/deg^2 not in 
kJ/mol/rad^2.


Cheers

Tom

--On Tuesday, November 17, 2009 07:49:01 -0500 Justin A. Lemkul 
jalem...@vt.edu wrote:





karan syal wrote:

Dear All,

I am looking for urea topology* (smith et al) *for gromos 96 force
field. I tried searching through user contributions in gromacs site but
couldnt find it. Is it possible for anyone who has already used it to
mail me their toplogy file?



If the parameters are published, you should probably contact the
corresponding author to see if they will share.

-Justin

--


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Virginia Tech
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] trjcat xtc files

[TJ Piggot]

You should use the -settime option, I think it should solve your problem.

Tom

--On Monday, November 02, 2009 00:21:31 -0800 Payman Pirzadeh 
ppirz...@ucalgary.ca wrote:



Your second guess is correct! I used grompp to restart (I had thought it
might provide me with the chance to change things if needed). I was
surprised initially when cat command did not work! The number of frames
were most of the time less than what it should be.
I also checked the 'trjcat -h'. I did not specifically understand how I
might be able to get over this issue. Any advices?

Payman

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Mark Abraham
Sent: Sunday, November 01, 2009 8:37 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] trjcat xtc files

Paymon Pirzadeh wrote:

Sorry,
My command line was:

 trjcat_d_mpi -f AFPI_Ih1010_54_58_Npt265_2.xtc
AFPI_Ih1010_54_58_Npt265_3.xtc AFPI_Ih1010_54_58_Npt265_4.xtc
AFPI_Ih1010_54_58_Npt265_5.xtc AFPI_Ih1010_54_58_Npt265_6.xtc -o
AFPI_Ih1010_54_58_Npt265_merged2-6.xtc

the _d_mpi is the suffix used for double precision and parallel
version of the installed gromacs.


OK so now we have some idea what you might be trying to do. The most
likely causes are that the first few trajectories have no frames, or
that each frame in the earlier trajectories is common to one in the last
trajectory. This might happen if you were using grompp to do restarts,
or have previously assigned duplicate times somehow. If so, find a
better workflow in future. Consult trjcat -h for clues on how to get
around this.

Mark


Payman

On Mon, 2009-11-02 at 15:08 +1100, Mark Abraham wrote:

Paymon Pirzadeh wrote:

Hello,
I am trying to concatenate several xtc files. When I use the trjcat, it
only writes the last file into the output file! where the problem could
be?

In your command line. Why didn't you tell us what it was? :-)

Mark
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Re: [gmx-users] Different temperatures for different groups, even with Nose-Hoover

[TJ Piggot]

 in the expansion of the constraint coupling matrix =
lincs_order              = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle          = 30
; Convert harmonic bonds to morse potentials =
morse                    = no

; NMR refinement stuff  =
; Distance restraints type: No, Simple or Ensemble =
disre                    = No
; Force weighting of pairs in one distance restraint: Equal or
Conservative =
disre_weighting          = Equal
; Use sqrt of the time averaged times the instantaneous violation =
disre_mixed              = no
disre_fc                 = 1000
disre_tau                = 1.25
; Output frequency for pair distances to energy file =
nstdisreout              = 100
--- end md2.mdp ---



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Re: [gmx-users] trjconv to process multiple types of molecules

[TJ Piggot]

Hi,

You need to use make_ndx to merge the MOL and ION into a new index group 
and then use that group in trjconv


Cheers

Tom

--On 07 October 2009 15:32 -0700 Yan Gao y1...@ucsd.edu wrote:


Hi There,

I have a problem using trjconv to get the trajectory.
I have three types of molecules: MOL, ION, SOL
and I want to convert only 2 types of them, how ever trjconv seems only
accept one input.
I want to keep only MOL and ION, and avoid the large amount of SOL, which
will reduce the analysis a lot.

Any suggestions will be appreciated!

Group 0 (  System) has 14260 elements
Group 1 ( MOL) has  2640 elements
Group 2 ( SOL) has 11580 elements
Group 3 ( ION) has40 elements

Warm regards,
Stone
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Re: [gmx-users] Z-position calculation

[TJ Piggot]

Hi,

You could also try g_bundle -z, it might do what you want.

Cheers

Tom

--On Tuesday, October 06, 2009 11:04:29 +0200 XAvier Periole 
x.peri...@rug.nl wrote:





g_traj with an index and playing with the different options.



On Oct 6, 2009, at 11:01 AM, Moutusi Manna wrote:

Dear all,
 I want to calculate the vertical position (Z-axis) of
different lipid head groups as a function of time.
 Looking forward for any suggestion.
 Thanks in advance,
 Moutusi Manna


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Re: [gmx-users] analyzing gromacs trajectories on VMD

[TJ Piggot]

If you just want to a visual inspection of the trajectory then the easiest 
way is to type:


vmd X.gro Y.xtc

Where X is the name of your structure file and Y the name of your trajectory

Tom

--On Thursday, September 17, 2009 14:51:57 -0700 Amit Choubey 
kgp.a...@gmail.com wrote:



hi everyone,


I want to analyze the gromacs trajectories using vmd, is there a quick
way of doing so ? Is there a reference for this?


Thank you
Amit 




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Re: [gmx-users] make_ndx help

[TJ Piggot]

1|12 merges the two groups into a new group

(112 will merge into a new group any atoms which are in both groups 1 and 
12, of which there are none in this case)


Tom

--On Wednesday, August 26, 2009 04:07:20 +0530 parthi...@ncbs.res.in wrote:


Hi

Anyone can please tell how to index 2 or more groups using make_ndx

eg: 1 protein
12 sol
13 NA+
i tried giving 112, which shows that the Group is empty

thanks in advance
Parthiban

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Re: [gmx-users] Gromacs in Parallel

[TJ Piggot]

I agree. Mpich 1 is very old, you should try mpich 2 or lam or openmpi.

Tom

--On Tuesday, August 11, 2009 09:16:54 +1000 Mark Abraham 
mark.abra...@anu.edu.au wrote:



Andrew Paluch wrote:

To whom this may concern,

I am receiving the following errors when attempting to run Gromacs in
parallel:

Making 1D domain decomposition 4 x 1 x 1
p2_21562:  p4_error: Timeout in establishing connection to remote
process: 0 p2_21562: (302.964844) net_send: could not write to fd=5,
errno = 32


where I am using mpich 1.2.7 for 64 bit processors.  From what I can
find, it seems as if this is a mpich issue and not an issue of Gromacs.
Has anyone else encountered such a problem?  Also, does anyone have any
suggestions for a solution?


Indeed, this is not a problem intrinsic to GROMACS. I'm not aware of
problems with particular MPI libraries, but you might try compiling
GROMACS with another such library. Whoever configured this machine should
probably look into the problem.

Mark
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Re: [gmx-users] atom name O3PB not found in residue ATP 340 while generating exclusions when running pdb2gmx

[TJ Piggot]

I agree with Justin that the way to do this is by adding a new entry to the 
.rtp file. The only point I would make is that as you seem to be missing 
the gamma phosphate and its oxygens would it not make more sense to start 
from an ADP topology? Also you should ask (or have asked) yourself why 
these atoms are missing in your start structure and do they need to be 
added back or are they missing for a purpose.


Tom

--On Thursday, May 07, 2009 06:59:21 -0400 Justin A. Lemkul 
jalem...@vt.edu wrote:





Una Bjarnadottir wrote:

Dear all,

I'm running a simulation of a structure which has part of ATP bound to
it so I'm using the -missing command when running pdb2gmx

pdb2gmx runs and lists the missing atoms and than it gives a fatal error
about missing atom name!

WARNING: atom O3PB is missing in residue ATP 340 in the pdb file
WARNING: atom APG is missing in residue ATP 340 in the pdb file
WARNING: atom O1PG is missing in residue ATP 340 in the pdb file
WARNING: atom O2PG is missing in residue ATP 340 in the pdb file
WARNING: atom O3PG is missing in residue ATP 340 in the pdb file
WARNING: atom H3PG is missing in residue ATP 340 in the pdb file
You might need to add atom H3PG to the hydrogen database of
residue ATP
in the file ff???.hdb (see the manual)

There were 17 missing atoms in molecule Protein_A
Number of bonds was 3730, now 3725
Generating angles, dihedrals and pairs...
Fatal error: atom name O3PB not found in residue ATP 340 while
generating exclusions



The [ exclusions ] are pre-defined in the force field .rtp file.  The
easiest way I can see to get around this is to make a local copy of the
.rtp file, make a new entry for your molecule based on the ATP entry
(deleting out whatever atoms are not present) and trying again, using a
new name for this partial ATP, in both the .rtp and .pdb files.

The -missing option, as described by pdb2gmx is dangerous for this
reason.

-Justin

How can I resolve this  first not done by -missing command?

Cheers, Una



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Problems with Jacobi diagonalization

[TJ Piggot]

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Re: [gmx-users] Triclinic water box for a protein MD

[TJ Piggot]

You might want to try a rombic dodecahedron box (an option in editconf).

Or you can run the simulation using a triclinic box hoping the images don't 
interact and then check after the simulation has finished using g_mindist 
-pi on the trajectory, bearing in mind if they do then you will have wasted 
a lot of time.


If you do want to use a triclinic box having a larger amount of water 
surrounding the complex may be advisable as this makes images interacting 
less likely


Tom

--On Friday, March 13, 2009 20:10:05 +0100 Tsjerk Wassenaar 
tsje...@gmail.com wrote:



Hi,

You have to make sure that you're molecule doesn't rotate. Otherwise
it will cause direct interactions over the PBC. The same holds true
for large conformational changes.

Cheers,

Tsjerk

On Fri, Mar 13, 2009 at 7:26 PM, Justin A. Lemkul jalem...@vt.edu wrote:



Lucio Montero wrote:


I want to simulate a protein complex using a triclinic box, because it
reduce my system size in 60%, and consequently the computing time. I
have read that using a triclinic box can give problems for a long MD if
the peptide has a whirl, but I don´t know if it is a problem for a
complex of ~ 530 aa (protein 1: 376 aa, protein 2: 132 aa, protein 3:
20 aa, complex size 64x64x104 Angstroms) surrounded by 12 Ângstroms of
water. I want to run the MD simulating 20 ns.


What problems have you read about?  Can you cite a source so we know what
you're talking about?

-Justin


Best regards,
Lucio Montero

 --
-- Lucio
Ricardo Montero Valenzuela
Laboratorio del Dr. Federico Sánchez
Ext. 27666
Departamento de Biología Molecular de Plantas
Instituto de Biotecnología, UNAM
Cuernavaca, Morelos, 62210




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ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] Triclinic water box for a protein MD

[TJ Piggot]

This looks great thanks, had meant to try and implement something like 
these restraints for ages but never got round to it, you know how it is ...


Tom

--On 13 March 2009 21:06 +0100 Tsjerk Wassenaar tsje...@gmail.com wrote:


Or, you use our server (http://haddock.chem.uu.nl/Squeeze/) to get an
optimally packed system and simulate it with the Gromacs 3.3.1 version
you can download from
http://nmr.chem.uu.nl/~tsjerk/GMX/gromacs-3.3.1-rtc.tgz
That version of gromacs has the roto-translational constraints
implemented that were developed by Andrea Amadei.
Mind that the server is fresh :) The paper is about to be submitted.
Unfortunately I haven't had time to dig into the GMX 4 code to
implement the rotational constraints yet. I wouldn't want to
compromise the performance :S

Cheers,

Tsjerk

On Fri, Mar 13, 2009 at 8:26 PM, TJ Piggot t.pig...@bristol.ac.uk wrote:

You might want to try a rombic dodecahedron box (an option in editconf).

Or you can run the simulation using a triclinic box hoping the images
don't interact and then check after the simulation has finished using
g_mindist -pi on the trajectory, bearing in mind if they do then you
will have wasted a lot of time.

If you do want to use a triclinic box having a larger amount of water
surrounding the complex may be advisable as this makes images interacting
less likely

Tom

--On Friday, March 13, 2009 20:10:05 +0100 Tsjerk Wassenaar
tsje...@gmail.com wrote:


Hi,

You have to make sure that you're molecule doesn't rotate. Otherwise
it will cause direct interactions over the PBC. The same holds true
for large conformational changes.

Cheers,

Tsjerk

On Fri, Mar 13, 2009 at 7:26 PM, Justin A. Lemkul jalem...@vt.edu
wrote:



Lucio Montero wrote:


I want to simulate a protein complex using a triclinic box, because it
reduce my system size in 60%, and consequently the computing time. I
have read that using a triclinic box can give problems for a long MD
if the peptide has a whirl, but I don´t know if it is a problem for a
complex of ~ 530 aa (protein 1: 376 aa, protein 2: 132 aa, protein 3:
20 aa, complex size 64x64x104 Angstroms) surrounded by 12 Ângstroms of
water. I want to run the MD simulating 20 ns.


What problems have you read about?  Can you cite a source so we know
what you're talking about?

-Justin


Best regards,
Lucio Montero

 
-- -- Lucio
Ricardo Montero Valenzuela
Laboratorio del Dr. Federico Sánchez
Ext. 27666
Departamento de Biología Molecular de Plantas
Instituto de Biotecnología, UNAM
Cuernavaca, Morelos, 62210


-
---

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Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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University of Bristol, UK.

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Junior UD (post-doc

Re: [gmx-users] OPLS-AA topologies for ATP/ADP.

[TJ Piggot]

Some of these charges look a bit suspect to me (eg the charge on the gamma 
phosphate). If you do not need to use OPLS then there is ATP included in 
the (united atom) gromos forcefields (see the top folder) and also ATP 
parameters available for the (all atom) Amber forcefields (see 
http://www.pharmacy.manchester.ac.uk/bryce/amber), all you have to do is 
convert them into a gromacs format


Tom

--On Thursday, February 26, 2009 08:33:06 -0800 Bruce D. Ray 
bruced...@yahoo.com wrote:




On Wednesday, February 25, 2009 12:06:20 AM, Lucio Ricardo Montero
Valenzuela

lucio...@ibt.unam.mx wrote:


Does anybody have the topology files for ATP and/or ADP for the OPLS-AA
forcefield?. If not, how can I parameterize this molecules?.
Best regards.
   Lucio Montero.

Lucio Ricardo Montero Valenzuela
Instituto de Biotecnologia, UNAM
Departamento de Biologia Molecular de Plantas
Av. Universidad 2001, Col. Chamilpa
Cuernavaca 62210
Mexico


I've not tested this at all, but from my attempts to add OPLS-AA to
topolbuild, I get the following that might be suitable for insertion in
the oplsaa rtp:

[ ATP ]
 [ atoms ]
   O9Popls_441  -0.635 0 ;O2
   O8Popls_441  -0.635 1 ;O2
   O7Popls_441  -0.635 2 ;O2
PGopls_445   0.072 3 ;P
   O6Popls_442  -0.286 4 ;OS
   O5Popls_441  -0.516 5 ;O2
   O4Popls_441  -0.516 6 ;O2
PBopls_440   0.280 7 ;P
   O3Popls_442  -0.250 8 ;OS
   O2Popls_441  -0.516 9 ;O2
   O1Popls_441  -0.51610 ;O2
PAopls_440   0.27611 ;P
   O5*opls_442  -0.31512 ;OS
   C5*opls_443   0.08513 ;CT
  H5*1opls_444   0.05914 ;HC
  H5*2opls_444   0.05915 ;HC
   C4*opls_174   0.11316 ;CT
   H4*opls_176   0.06517 ;HC
   O4*opls_186  -0.34818 ;OS
   C1*opls_193   0.16019 ;CO
   H1*opls_194   0.08420 ;HC
N9opls_354B -0.24521 ;NA
C8opls_353   0.09222 ;CK
H8opls_359   0.10023 ;H5
N7opls_352  -0.23324 ;NB
C5opls_350   0.14525 ;CB
C6opls_351   0.14726 ;CA
N6opls_356  -0.34127 ;N2
   H61opls_357   0.14428 ;H
   H62opls_358   0.14429 ;H
N1opls_346  -0.21930 ;NC
C2opls_347   0.12031 ;CQ
H2opls_355   0.06632 ;H5
N3opls_348  -0.21833 ;NC
C4opls_349   0.15934 ;CB
   C2*opls_174   0.12735 ;CT
   H2*opls_176   0.10036 ;HC
   O2'opls_171  -0.38537 ;OH
   H2'opls_172   0.21038 ;HO
   C3*opls_174   0.11339 ;CT
   H3*opls_176   0.06540 ;HC
   O3'opls_171  -0.38641 ;OH
   H3'opls_172   0.21042 ;HO
 [ bonds ]
PG   O9P
PG   O8P
PG   O7P
   O6PPG
PB   O6P
PB   O5P
PB   O4P
   O3PPB
PA   O3P
PA   O2P
PA   O1P
PA   O5*
   O5*   C5*
   C5*   C4*
   C5*  H5*1
   C5*  H5*2
   C4*   O4*
   C4*   H4*
   C4*   C3*
   O4*   C1*
   C1*N9
   C1*   H1*
   C1*   C2*
N9C8
C8H8
C8N7
N7C5
C5C6
C5C4
C6N6
N6   H61
N6   H62
C6N1
N1C2
C2H2
C2N3
N3C4
C4N9
   C2*   C3*
   C2*   H2*
   C2*   O2'
   O2'   H2'
   C3*   H3*
   C3*   O3'
   O3'   H3'


Please let me know if this actually works for computations.
Charges were derived from the .mol2 file generated by Sybyl.


Sincerely,


--
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273



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--
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t.pig...@bristol.ac.uk
University of Bristol, UK.

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Re: [gmx-users] OPLS-AA topologies for ATP/ADP.

[TJ Piggot]

Sorry realised I posted the amber ATP link wrong, it is without the ) at 
the end:


http://www.pharmacy.manchester.ac.uk/bryce/amber

Tom

--On Thursday, February 26, 2009 17:15:22 + TJ Piggot 
t.pig...@bristol.ac.uk wrote:



Some of these charges look a bit suspect to me (eg the charge on the
gamma phosphate). If you do not need to use OPLS then there is ATP
included in the (united atom) gromos forcefields (see the top folder) and
also ATP parameters available for the (all atom) Amber forcefields (see
http://www.pharmacy.manchester.ac.uk/bryce/amber), all you have to do is
convert them into a gromacs format

Tom

--On Thursday, February 26, 2009 08:33:06 -0800 Bruce D. Ray
bruced...@yahoo.com wrote:



On Wednesday, February 25, 2009 12:06:20 AM, Lucio Ricardo Montero
Valenzuela

lucio...@ibt.unam.mx wrote:


Does anybody have the topology files for ATP and/or ADP for the OPLS-AA
forcefield?. If not, how can I parameterize this molecules?.
Best regards.
   Lucio Montero.

Lucio Ricardo Montero Valenzuela
Instituto de Biotecnologia, UNAM
Departamento de Biologia Molecular de Plantas
Av. Universidad 2001, Col. Chamilpa
Cuernavaca 62210
Mexico


I've not tested this at all, but from my attempts to add OPLS-AA to
topolbuild, I get the following that might be suitable for insertion in
the oplsaa rtp:

[ ATP ]
 [ atoms ]
   O9Popls_441  -0.635 0 ;O2
   O8Popls_441  -0.635 1 ;O2
   O7Popls_441  -0.635 2 ;O2
PGopls_445   0.072 3 ;P
   O6Popls_442  -0.286 4 ;OS
   O5Popls_441  -0.516 5 ;O2
   O4Popls_441  -0.516 6 ;O2
PBopls_440   0.280 7 ;P
   O3Popls_442  -0.250 8 ;OS
   O2Popls_441  -0.516 9 ;O2
   O1Popls_441  -0.51610 ;O2
PAopls_440   0.27611 ;P
   O5*opls_442  -0.31512 ;OS
   C5*opls_443   0.08513 ;CT
  H5*1opls_444   0.05914 ;HC
  H5*2opls_444   0.05915 ;HC
   C4*opls_174   0.11316 ;CT
   H4*opls_176   0.06517 ;HC
   O4*opls_186  -0.34818 ;OS
   C1*opls_193   0.16019 ;CO
   H1*opls_194   0.08420 ;HC
N9opls_354B -0.24521 ;NA
C8opls_353   0.09222 ;CK
H8opls_359   0.10023 ;H5
N7opls_352  -0.23324 ;NB
C5opls_350   0.14525 ;CB
C6opls_351   0.14726 ;CA
N6opls_356  -0.34127 ;N2
   H61opls_357   0.14428 ;H
   H62opls_358   0.14429 ;H
N1opls_346  -0.21930 ;NC
C2opls_347   0.12031 ;CQ
H2opls_355   0.06632 ;H5
N3opls_348  -0.21833 ;NC
C4opls_349   0.15934 ;CB
   C2*opls_174   0.12735 ;CT
   H2*opls_176   0.10036 ;HC
   O2'opls_171  -0.38537 ;OH
   H2'opls_172   0.21038 ;HO
   C3*opls_174   0.11339 ;CT
   H3*opls_176   0.06540 ;HC
   O3'opls_171  -0.38641 ;OH
   H3'opls_172   0.21042 ;HO
 [ bonds ]
PG   O9P
PG   O8P
PG   O7P
   O6PPG
PB   O6P
PB   O5P
PB   O4P
   O3PPB
PA   O3P
PA   O2P
PA   O1P
PA   O5*
   O5*   C5*
   C5*   C4*
   C5*  H5*1
   C5*  H5*2
   C4*   O4*
   C4*   H4*
   C4*   C3*
   O4*   C1*
   C1*N9
   C1*   H1*
   C1*   C2*
N9C8
C8H8
C8N7
N7C5
C5C6
C5C4
C6N6
N6   H61
N6   H62
C6N1
N1C2
C2H2
C2N3
N3C4
C4N9
   C2*   C3*
   C2*   H2*
   C2*   O2'
   O2'   H2'
   C3*   H3*
   C3*   O3'
   O3'   H3'


Please let me know if this actually works for computations.
Charges were derived from the .mol2 file generated by Sybyl.


Sincerely,


--
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273



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Re: [gmx-users] eigenvalues

[TJ Piggot]

So just to make sure i got this correct, when looking at the cosine content 
of the principal components i should look at the whole trajectory? Do i 
need to include the initial relaxation in the first few ns of the 
production simulation?


If there is a high cosine content for the whole trajectory is there 
anything else to be done (if i want to look at the low frequency motions of 
the trajectory) except for simulate for longer (i have a very large system 
so not the favoured option!)?


As you say it seems that lots of people use PCA on short trajectories, even 
of large systems, which to me is confusing


Thanks for any insights you can give

Tom

--On Saturday, January 10, 2009 11:49:18 +0100 Tsjerk Wassenaar 
tsje...@gmail.com wrote:



Hi Sanjay,

Imagine yourself zig-zagging along a line from one place to another.
If you look at you're motion (and the variance), you'll find that if
you only look at blocks most of it is explained by the zig-zag and
nicely periodic (no cosine content as in Berk Hess' paper). Good, you
think. But if you look at the whole travel, the most important
contribution is the going from one place to another, and if you look
at you're displacement over time with respect to the mean, that will
give you half a cosine. The fact that results in a block do not fit a
cosine does not take away the fact that you're still in the process of
relaxation. I know it's not what you want to hear, but I've seen it
happen to a complex of 600 residues, where relaxation took more than
30 ns. I also know that people often do PCA on short time
trajectories, but it's not the proper thing to do.

Cheers,

Tsjerk

On Sat, Jan 10, 2009 at 7:34 AM,  sanja...@iitb.ac.in wrote:

Hi Tsjerk,
thanks
actually my protein is quite larg (509 aa).i had divided my trajectory in
different part and according to your suggestion i calculated
cosine-content for all, and find that trajectory from 5to15 ns and
18to25ns having cosine value very less about 0.03 in both cases(with and
without ligands), while other combination showing higher values (0.6).so
i think my system is Ist converges around 5ns and maintaining it up to 15
ns after that it may be few conformational fluctuation occurring and
finally it get stabilized from 18to15ns.may that part 15to18ns trajectory
is transition period between to conformational fluctuation. i have also
calculated temp. and pressure during whole simulation and i find that it
is exact Gaussian between 5to25ns.so my confusion is whether i take my
trajectory for ED analysis is from 5to15 or 18to25 or whole from 5to25,
but 5to25 showing value of cosine 0.6.

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Re: [gmx-users] Analyzing a trajectory split over multiple files

[TJ Piggot]

Just as a note most analysis tools have a -noxvgr option to output the 
results without any of the formatting information for grace.


Also I still think the easiest way to solve your problem is to just 
initially use trjcat to concatenate your trajectory, then run the analysis 
on this.


Tom

--On Friday, November 28, 2008 05:06:31 +0530 Suman Chakrabarty 
[EMAIL PROTECTED] wrote:



On Fri, Nov 28, 2008 at 4:24 AM, Nicolas [EMAIL PROTECTED] wrote:

Suman Chakrabarty a écrit :

It would have been much easier if there was some way to concatenate
the multiple .xvg files easily. Also, the analysis programs should be
able to export the output data in raw 2 (or more) column format
without all the formatting statements as an option.



Actually, there is:

grep -v ^# *.xvg  concatenate.xvg

The -v ^# will skip all the comment lines of your xvg files. Of course,
this assumes that your xvg files are correctly named, i.e. file01.xvg,
file02.xvg, etc. With a short shell script, you can easily re-add the
comments at the beginning of your concatenate file, renumber the frames
correctly, etc. It is more convenient to write a Python or a Perl script
to do this kind of stuff, though.

Nicolas




Thank you very much! I always knew there must be something smart to be
done. I should now delve into the nitty-gritty of scripting. grep
seems to be a particularly useful tool! :)


Regards,
Suman.




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[EMAIL PROTECTED]
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Re: [gmx-users] doubt about the oplsaa topology

[TJ Piggot]

Check out ffoplsaanb.itp to see which name (opls_XXX) corresponds to which 
bond type (ie. what you are seeing in ffoplsaabon.itp)


Tom

--On Friday, September 12, 2008 17:41:48 -0400 Serena Leone 
[EMAIL PROTECTED] wrote:



Hello all,

I am trying to build the topology for an oligosaccharide to be used,
together with a peptide, in a  simulation with oplsaa (apparently, from
the discussions in the last days, this should be the best choice...).
Now, I had a .top from prodrg that I previously modified and used, and I
was starting rewriting on it the new .top for the oplsaa. After renaming
all the atoms according to the ffoplsaa.atp, ( i will figure out later
how to include the missing non polar Hs), i wanted to check that all the
bonds in this molecule were described in the ffoplsaabon.itp (i have
sulfate groups) BUT, when I opened the ffoplsaabon.itp, I noticed that
the atom names don't correspond to the types described in the .atp
(opls_n), but more likely to the names in any other gro force field. I'm
confused... anybody can explain me this contradiction?

thanks a lot...

great day to all...

serena
--

Serena Leone, Ph.D.
Brigham and Women's Hospital
Harvard Medical School
Channing Laboratory EBRC 609
221 Longwood Avenue
Boston, MA 02115
(tel)  617-732-8586






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Re: [gmx-users] which force field for a protein-protein complex?

[TJ Piggot]

Hi,

Personally i would use an AMBER forcefield, because the following link has 
parameters for both the ligands you have in your system, which can be 
tricky and time consuming to derive accurately.


http://www.pharmacy.manchester.ac.uk/bryce/amber

All you need to do is convert the Amber file formats into Gromacs ones, to 
do this by hand consult the Gromacs manual (or you may be able to use the 
ambconv tool which can be found on the user contribution section of the 
Gromacs website).


Also make sure you do not use ffgmx as it is deprecated.

Tom

--On Friday, September 05, 2008 15:06:21 +0200 Paula González-Rubio 
[EMAIL PROTECTED] wrote:




Hello there,

I would like to do a MD of a protein-protein complex (both with their
ligands) so I'm looking for some advise regarding the best force field
for simulate my system. For more details, it consists on a ADP-ribosylase
(which ligand is the NAD) and a small G protein (GDP binded), we want to
see what is the role of a loop in the formation of the complex and on the
ADP-ribosilation of the small G protein.

Does any one have a good idea of an appropiate force field for this kind
of systems ? Do you think gromos 43A1 or ffgmx could be an option?

Thanks a lot in advance!
Paula


-- ! NEW email !!

[EMAIL PROTECTED]


*** NEW ADDRESS **
Paula GONZALEZ-RUBIO
PhD Candidate
DSIMB INTS, INSERM UMR-S726
6 rue Alexandre Cabanel 75015 Paris
Tel : +33(1) 44 49 30 00 Fax : +33(1) 47 34 74 31
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[EMAIL PROTECTED]
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Re: [gmx-users] Parameters for DNA bases

[TJ Piggot]

If you really want to use OPLS/AA then you can find DNA parameters on the 
Gromacs website using the following link.


http://www.gromacs.org/component/option,com_docman/task,doc_details/gid,45/Itemid,26/

However i am not sure that these parameters are well tested and i am not 
sure if they have been used in many/any published works. Like Justin said 
the AMBER forcefields would be a better option unless you need OPLS/AA for 
a specific reason, for more info on the AMBER forcefields in Gromacs see:


http://chemistry.csulb.edu/ffamber/

Hope this helps

Tom

--On Tuesday, September 02, 2008 21:24:45 -0400 Justin A. Lemkul 
[EMAIL PROTECTED] wrote:





Jeff Woodford wrote:

Hi all,

Forgive me if this is a stupid question, but:

I am attempting to simulate the interaction between a peptide and a DNA
strand using the OPLS/AA force field.  However the parameters for the
DNA bases don't appear to be included.  Where might I find these
parameters suitable for adapting to GROMACS?




Any particular motivation for using OPLS-AA?  The AMBER force fields
include both DNA and protein.

-Justin



Thanks in advance,

-Jeff



Jeffrey N. Woodford

Associate Professor of Chemistry

Eastern Oregon University

Tel: 541-962-3321

Fax: 541-962-3873






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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Dealing with residues not in the topology database

[TJ Piggot]

In addition to what Justin has said there are parameters for GTP to use 
with the amber forcefields, see:


http://www.pharmacy.manchester.ac.uk/bryce/amber#cof

Obviously you need to convert these from an amber format to a gromacs one. 
Do note that an additional atom type for the terminal anionic oxygens is 
needed so the conversion using the contributed tools may not be straight 
forward


Tom

--On Wednesday, June 25, 2008 13:57:23 -0400 Justin A. Lemkul 
[EMAIL PROTECTED] wrote:





Travis Craddock wrote:

Hello,

I am a new GROMACS user.  My aim is to simulate the protein tubulin with
a GTP molecule present.  When attempting to create a topology file I
receive a Fatal Error stating that the Residue GTP is not found in the
topology database.  I understand that GTP is not parameterized for the
force field that I am using, and from what I have read of previous
posts, creating a new *.itp file is rather complicated and not
recommended for new users.  As such, I would like to ask if anyone can
recommend a starting point to learn more about simulations in GROMACS so
that I can eventually learn how to run my intended simulation, i.e.
tutorials dealing with the creation of *.itp files, or previous work
that outlines some of the details.  Thank-you.




Doing a simple Google search for Gromacs tutorial should yield some
good results.  Take a look at the wiki site as well, there's lots of
information there.

Creation of .itp files will require thorough knowledge of how the
original force field was derived, and then applying that procedure to
your molecule.  Parameters for GTP under Gromos96 were discussed across
this list not too long ago (search the archive), and if you're using
Amber, you can use tools to create a GAFF-parameterized molecule using
antechamber and convert it to .itp format using tools available in the
User Contributions on the Gromacs site.

-Justin


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Re: [gmx-users] TEE-REX installation error

[TJ Piggot]

Thanks for the answer, configuring with --enable-mpi solves the problem.

Just to note it was not totally clear from the TEE-REX documentation that 
this had to be the case, however suppose i should have thought about it and 
realised replica exchange is usually ran on more than one processor!


Tom

--On Tuesday, June 10, 2008 02:14:40 +1000 Mark Abraham 
[EMAIL PROTECTED] wrote:



TJ Piggot wrote:

Hi,

I am trying to install the TEE-REX patch for gromacs 3.3.1 and am
getting the following make error:

cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include
-DGMXLIBDIR=\/home/tp1821/Gromacs/teerex/share/top\ -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -MT gmx_parallel_3dfft.lo -MD -MP -MF
.deps/gmx_parallel_3dfft.Tpo -c gmx_parallel_3dfft.c -o
gmx_parallel_3dfft.o
if /bin/sh ../../libtool --mode=compile cc -DHAVE_CONFIG_H -I. -I.
-I../../src  -I../../include
-DGMXLIBDIR=\/home/tp1821/Gromacs/teerex/share/top\   -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -MT qm_gaussian.lo -MD -MP -MF
.deps/qm_gaussian.Tpo -c -o qm_gaussian.lo qm_gaussian.c; \
then mv -f .deps/qm_gaussian.Tpo .deps/qm_gaussian.Plo; else rm -f
.deps/qm_gaussian.Tpo; exit 1; fi
if /bin/sh ../../libtool --mode=compile cc -DHAVE_CONFIG_H -I. -I.
-I../../src  -I../../include
-DGMXLIBDIR=\/home/tp1821/Gromacs/teerex/share/top\   -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -MT gmx_fft_fftw3.lo -MD -MP -MF
.deps/gmx_fft_fftw3.Tpo -c -o gmx_fft_fftw3.lo gmx_fft_fftw3.c; \
then mv -f .deps/gmx_fft_fftw3.Tpo .deps/gmx_fft_fftw3.Plo; else rm
-f .deps/gmx_fft_fftw3.Tpo; exit 1; fi
cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include
-DGMXLIBDIR=\/home/tp1821/Gromacs/teerex/share/top\ -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -MT teerex.lo -MD -MP -MF .deps/teerex.Tpo -c
teerex.c -o teerex.o
teerex.c: In function `init_TEEREX':
teerex.c:167: warning: implicit declaration of function `MPI_Gather'
teerex.c:167: error: `MPI_FLOAT' undeclared (first use in this function)
teerex.c:167: error: (Each undeclared identifier is reported only once
teerex.c:167: error: for each function it appears in.)
teerex.c:167: error: `MPI_COMM_WORLD' undeclared (first use in this
function)
teerex.c:244: warning: implicit declaration of function `MPI_Barrier'


These are occurring because teerex.c is expecting to be part of an MPI
installation of GROMACS, and yours isn't. Thus either the installation
documentation of TEE-REX, or your following of it, is suspect :-) I know
nothing about TEE-REX, but your first move after checking their
documentation again should be a make distclean and then to reconfigure
GROMACS with the --enable-mpi flag.

Mark
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[gmx-users] TEE-REX installation error

[TJ Piggot]

Hi,

I am trying to install the TEE-REX patch for gromacs 3.3.1 and am getting 
the following make error:


cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include 
-DGMXLIBDIR=\/home/tp1821/Gromacs/teerex/share/top\ -O3 
-fomit-frame-pointer -finline-functions -Wall -Wno-unused 
-funroll-all-loops -MT gmx_parallel_3dfft.lo -MD -MP -MF 
.deps/gmx_parallel_3dfft.Tpo -c gmx_parallel_3dfft.c -o gmx_parallel_3dfft.o
if /bin/sh ../../libtool --mode=compile cc -DHAVE_CONFIG_H -I. -I. 
-I../../src  -I../../include 
-DGMXLIBDIR=\/home/tp1821/Gromacs/teerex/share/top\   -O3 
-fomit-frame-pointer -finline-functions -Wall -Wno-unused 
-funroll-all-loops -MT qm_gaussian.lo -MD -MP -MF .deps/qm_gaussian.Tpo 
-c -o qm_gaussian.lo qm_gaussian.c; \
then mv -f .deps/qm_gaussian.Tpo .deps/qm_gaussian.Plo; else rm -f 
.deps/qm_gaussian.Tpo; exit 1; fi
if /bin/sh ../../libtool --mode=compile cc -DHAVE_CONFIG_H -I. -I. 
-I../../src  -I../../include 
-DGMXLIBDIR=\/home/tp1821/Gromacs/teerex/share/top\   -O3 
-fomit-frame-pointer -finline-functions -Wall -Wno-unused 
-funroll-all-loops -MT gmx_fft_fftw3.lo -MD -MP -MF 
.deps/gmx_fft_fftw3.Tpo -c -o gmx_fft_fftw3.lo gmx_fft_fftw3.c; \
then mv -f .deps/gmx_fft_fftw3.Tpo .deps/gmx_fft_fftw3.Plo; else rm -f 
.deps/gmx_fft_fftw3.Tpo; exit 1; fi
cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include 
-DGMXLIBDIR=\/home/tp1821/Gromacs/teerex/share/top\ -O3 
-fomit-frame-pointer -finline-functions -Wall -Wno-unused 
-funroll-all-loops -MT teerex.lo -MD -MP -MF .deps/teerex.Tpo -c teerex.c 
-o teerex.o

teerex.c: In function `init_TEEREX':
teerex.c:167: warning: implicit declaration of function `MPI_Gather'
teerex.c:167: error: `MPI_FLOAT' undeclared (first use in this function)
teerex.c:167: error: (Each undeclared identifier is reported only once
teerex.c:167: error: for each function it appears in.)
teerex.c:167: error: `MPI_COMM_WORLD' undeclared (first use in this 
function)

teerex.c:244: warning: implicit declaration of function `MPI_Barrier'
make[3]: *** [teerex.lo] Error 1
make[3]: *** Waiting for unfinished jobs
cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include 
-DGMXLIBDIR=\/home/tp1821/Gromacs/teerex/share/top\ -O3 
-fomit-frame-pointer -finline-functions -Wall -Wno-unused 
-funroll-all-loops -MT qm_gaussian.lo -MD -MP -MF .deps/qm_gaussian.Tpo -c 
qm_gaussian.c -o qm_gaussian.o
cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include 
-DGMXLIBDIR=\/home/tp1821/Gromacs/teerex/share/top\ -O3 
-fomit-frame-pointer -finline-functions -Wall -Wno-unused 
-funroll-all-loops -MT gmx_fft_fftw3.lo -MD -MP -MF .deps/gmx_fft_fftw3.Tpo 
-c gmx_fft_fftw3.c -o gmx_fft_fftw3.o
make[3]: Leaving directory 
`/home/tp1821/Gromacs/gromacs-3.3.1-teerex/src/mdlib'

make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/tp1821/Gromacs/gromacs-3.3.1-teerex/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/tp1821/Gromacs/gromacs-3.3.1-teerex/src'
make: *** [all-recursive] Error 1


I am using the gcc 3.4.6 compiler on a CentOS 4 linux box and also gromacs 
3.3.1 without the TEE-REX patch installs fine.


Thanks for any advice you can give me to fix this problem.

Tom Piggot

--
TJ Piggot
[EMAIL PROTECTED]
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Re: [gmx-users] GTP topology generation in OPLS-AA force field

[TJ Piggot]

Bear in mind that parameterising a new molecule is an advanced topic. Maybe 
an easier solution would be to use another forcefield which already has a 
GTP topology. For example the amber forcefields I know to have GTP 
parameters available, all you would have to do is to convert them into 
GROMACS format.


Tom

--On Wednesday, April 30, 2008 06:49:35 -0400 Justin A. Lemkul 
[EMAIL PROTECTED] wrote:



Quoting Shankar Prasad Kanaujia [EMAIL PROTECTED]:


Dear gmx-users,
I want to run MD for my protein with GTP compound.
I am using OPLS-AA force field. How can I generate
the topology file for GTP in OPLS-AA force field ?


Derive parameters consistent with the methods used to generate the
original force field.

http://wiki.gromacs.org/index.php/Parameterization

-Justin



Thanking you all for your kind support and suggestions.

---
Yours Sincerely,
Shankar Prasad Kanaujia
Research Student
C/O - Dr. K. Sekar
Bioinformatics Center, Department of SERC
IISc, Bangalore - 12, INDIA.
Office Phone: 2469, 3059
Mobile: 9845631581



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This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

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Department of Biochemistry
Virginia Tech
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[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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Re: [gmx-users] how to calculate redisue wise RMSD in gromacs?

[TJ Piggot]

Also try g_rmsf -h. This might be what you are looking for.

Tom

--On Friday, March 28, 2008 15:07:02 +1100 Mark Abraham 
[EMAIL PROTECTED] wrote:



[EMAIL PROTECTED] wrote:

Dear friends,
 I have carried out a simulation of a protein in solution and want to
analyse redisue wise root-mean-square-deviation (RMSD) of the protein. As
far as I know,   RMSD can be calculated by g_rms, which gives RMSD as a
function of time, but what I expect is RMSD as a function of residue
number. It's said that AMBER has this function. I wonder whether gromacs
can do this also.


Check out g_rms -h, in particular the -ng option. I expect you can use
this in concert with an index file that has a group for each residue.

Mark
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Re: [gmx-users] How to create three different zones to minimize energy of a enzyme?

[TJ Piggot]

I suppose it should be mentioned that even with an average desktop computer 
it should be more than feasible to minimise the whole of your enzyme 
system. If you want to simulate the system for long periods of time then 
that is a different question.


Tom

--On Wednesday, March 19, 2008 08:34:29 +0100 Tsjerk Wassenaar 
[EMAIL PROTECTED] wrote:



Hi Lacerda,

You should be cautious in the interpretation of your results. Your
active site will only be minimized in potential energy in the context
of your frozen surface and your restraint internal degrees of freedom.
You should be very confident that your surface is about correct and
your internal dof are approximately correct in relation to the state
of the active site you're interested in. And that's only in terms of
energy minimization. If it comes to dynamics, using this approach you
would disallow the larger amplitude motions of your system and
therefore the coupling with the active site, or actually the
meaningful dynamics of the active site.

Now, say you want to energy minimize the active site because you put a
ligand in. In most cases, the ligand will alter the ensemble. It may
very well commute with residues on the surface (allostery?). If you
constrain residues which are to respond to the ligand you will add
strain to the system which wouldn't be there in the real
(unconstrained) thing. You can imagine how this works by placing two
magnets together with the equal poles, while constraining them, rather
than leaving one to respond to the other.

Hope this helps,

Tsjerk


On Wed, Mar 19, 2008 at 1:51 AM, Mark Abraham [EMAIL PROTECTED]
wrote:

Evanildo Júnior wrote:
  Dear gmx-users,
 
  I would like to minimize the potential energy of the active site of an
  enzyme. Because I do not have too much computer power to perform a
  full enzyme calculation, I need to create three different zones in
  which the calculation will take place. The first one is  the outer
  boundary of the enzyme that will remain frozen during the calculation.

 Look for freeze groups in the manual. They work with MD and I'm
 guessing they also work with EM.


  The second one is
  a transition region between the active site region and the outer
  boundary, whose atoms will receive a parabolic potential in order to
  move just a little bit.

 Use position restraints.


  The last one is the active site itself which
  will be freely minimized. I would like to know how do I implement it
  in practice. Does anyone has a Gromacs script for this task? The other
  question is how do I freeze only the C-alpha chain?

 Apply a freeze group only to the C-alpha atoms. You'll need to use
 make_ndx to make the group and give that index file to grompp as well as
 the usual stuff.

 If you're as new to GROMACS as you sound like you might be, you should
 do some tutorial material and read the first few chapters of the manual
 thoroughly. Doing the above would not be a good way to get your first
 exposure to using GROMACS.

 Mark
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Re: [gmx-users] selecting residues which are within cutoff distances

[TJ Piggot]

I think g_dist with the option -dist will do what you want

Tom

--On Thursday, March 13, 2008 16:20:15 +0100 maria goranovic 
[EMAIL PROTECTED] wrote:



Hello Folks,

I have a protein trajectory to analyze. The goal is to find all residues
within a 6 Angstrom radius of another residue, and list their names (for
example) over a trajectory. How can one do this ? I tried using g_mdmat.
However, the eps generated by using xps2pm does not really convey too
much perhaps because of bad resolution ?

Is there any other way ?

Thank you in advance

-Maria
--
Maria G.
Technical University of Denmark
Copenhagen




--
TJ Piggot
[EMAIL PROTECTED]
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Re: [gmx-users] Problem with using distance restraints (disre) with PBC

[TJ Piggot]

Hi i have modified the src to stop harmonic potentials being put into the 
graph (as was suggested to me by Berk Hess, see below for the modification 
you need to make). I would be imagine this is also possible to do for 
distance/orientation restraints, however i only know a small amount of 
programming so you will need someone else to help you here. Here is the 
change i have made and it works fine for me:


A real fix would then be adding
i!=F_HARMONIC 
to the if statement on line 272 of src/gmxlib/mshift.c
and recompiling Gromacs, such that the harmonic potentials
are not put into the graph.

Tom



--On Thursday, March 06, 2008 12:50:18 +1000 Mitchell Stanton-Cook 
[EMAIL PROTECTED] wrote:



Hi Tom,

Have you modified the src? As far as I know this has not been done in 331
or 332. I'm unsure of 333. I would be interested in the patch. As far as
I know the problem is due to the the distance/orientation restraints
being placed in the bonded graph. There was a bit of chatter on the
developers list in 2007 about this but I haven't heard much else.

For my system I was using a truncated dodecahedron box. The box vector
1/2d was my biggest problem. I simply changed to a triclinic box without
too much cost. However I think I could grab an extra 300ps/day if I had
an actual fix.


Cheers

Mitch

TJ Piggot wrote:

I agree with increasing the size of the box (if seeing inconsistent
shifts, as i should have mentioned in my previous post) and in this
case it is practical to do as the system is quite small. However (just
for future reference) if the problem were in a much larger system (as
it is in my case) then it may be more suitable to modify the source
code to avoid increasing the size of the system simulated.

Tom

--On Thursday, March 06, 2008 11:52:01 +1000 Mitchell Stanton-Cook
[EMAIL PROTECTED] wrote:


I have had a similar problem with orientation restraints.

Are the residues far is space? Are you getting inconsistent shifts?
If so
-

If so re-define your box size so that the shortest box vector is greater
than the distance restraint residue + some tolerance.

I also noticed -

[ distance_restraints ]
;ai aj  typeindex   type   low up1 up2 fac
 9 413   1 0 1   8.18 8.18  10.0
 1.0

Have you defined the low up and up2 in the correct units?

Cheers

Mitch

TJ Piggot wrote:

Hi,

Firstly I would strongly reiterate what Mark said. I would make sure
the distance restraints are causing your problem. Again as Mark said
make sure you can simulate your system without the distance
restraints, and then I would try to simulate the system with distance
restraints and with a much larger box of water surrounding your
peptide. Here you should also be able to overcome the problem (if it
is this problem) with a large enough distance between periodic images.

If you can then confirm what you have suspected to be the problem you
will need to modify the source code slightly. If you search the list
(searching for inconsistent shifts using multiple bonds type 6) you
can see the changes you need to make, as suggested by Berk Hess to me
when i had this problem with bond type 6.


Hope this helps

Cheers

Tom

--On Wednesday, March 05, 2008 17:16:23 -0500 Grace Li
[EMAIL PROTECTED] wrote:


Hello,
I am having some trouble using distance restraints. My goal is to
apply a
harmonic potential to the distance between two atoms in a short
peptide
(35 residues). Doing simulations in vacuo, both of the following
techniques worked to restrain the distance. Also, both techniques
worked
for simulations in water without periodic boundary conditions. As soon
 as I include pbc = xyz in my .mdp file and use PME for the
electrostatics,  my simulation crashes (producing step0.pdb and
step-1.pdb). I am assuming this is because GROMACS is using the
distance
to the image of the other atom, not the actual distance in the box? Is
there any way of getting around PBC for distance restraints?

Specifically, I have used the following:

1. I have tried using bonds type 6 in my topology:
[ bonds ]
;  aiaj funct c0 c1 c2 c3
   9   413 6 8.18  421.54

2. When using distance restraints, I added the following lines to my
topology file:
[ distance_restraints ]
;ai aj  typeindex   type   low up1 up2 fac
 9 4131 0 1   8.18 8.18  10.0
 1.0

In the case of using [ distance_restraints ] in the topology file, I
 have
added the following lines to my .mdp file:
disre = simple
disre_fc = 421.54
disre_weighting = equal
disre_tau = 0
(and various other values of the force constant, disre_fc, but in all
cases the run crashes).

Thanks for any suggestions!
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Re: [gmx-users] DNA adduct simulation: grompp error

[TJ Piggot]

For the missing whitespace warning you need cpp = /lib/cpp -traditional in 
you .mdp file.


For the error you most likely do not have an #ifdef _FF_AMBER statement in 
you spc.itp file.


These have both been discussed on the list before so search there for more 
details and also the ffamber website:


http://chemistry.csulb.edu/ffamber/

As for your choice of forcefield (and parameterising your adduct) this has 
been discussed numerous times before (including recently) so again search 
the mailing list or the gromacs wiki.


Tom

--On Wednesday, February 20, 2008 16:09:32 +0100 Nathalie Geneste 
[EMAIL PROTECTED] wrote:



Dear users,

I have some problems to launch a simulation with my molecular system
including 2 strands DNA + benzo[a]pyrene adduct.
After some trials with default gromacs force fields, I downloaded
ffamber99.

I have 2 problems:

1) my benzo[a]pyrene adduct is not recognized by ffamber99. Could you
propose me a force field compatible with my system ?

2) If I ignore my adduct, we obtained with success my topolgy files but
now I got the following error with grompp:
...
checking input for internal consistency...
calling /usr/bin/cpp...
In file included from /usr/share/gromacs/top/ffamber99.itp:20,
 from 1AXV_mod4.top:11:
/usr/share/gromacs/top/ffamber99bon.itp:518:22: warning: missing
whitespace after the macro name
/usr/share/gromacs/top/ffamber99bon.itp:520:22: warning: missing
whitespace after the macro name
/usr/share/gromacs/top/ffamber99bon.itp:521:22: warning: missing
whitespace after the macro name
/usr/share/gromacs/top/ffamber99bon.itp:524:21: warning: missing
whitespace after the macro name
/usr/share/gromacs/top/ffamber99bon.itp:535:19: warning: missing
whitespace after the macro name
processing topology...
Generated 2628 of the 2628 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2628 of the 2628 1-4 parameter combinations
Cleaning up temporary file gromppEkqU9b
---
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 1108

Fatal error:
[ file /usr/share/gromacs/top/spc.itp, line 41 ]:
 Atom index (1) in settles out of bounds (1-0)
---

Does anybody has an explanation ?

Regards,
Nathalie


--

**
Dr. N. GENESTE
Groupe LPTC
ISM - UMR 5255 CNRS
Université Bordeaux I
Phone.: 05 40 00 28 43
Fax: 05 40 00 22 67

**
Nouvelle adresse:
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[EMAIL PROTECTED]
University of Bristol, UK.

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Re: [gmx-users] AMBER ff99SB port problems

[TJ Piggot]

Hi,

You need to make sure you have an #ifdef _FF_AMBER statement in the spc.itp 
file for it to work correctly, as Mark has suggested. This has been 
discussed on the list before.


Tom

--On Friday, December 07, 2007 17:57:47 + Shozeb Haider 
[EMAIL PROTECTED] wrote:



Hi,

I was wondering if any has expertise in using Amber ff99SB port (Pande's
lab). I am currently using port for 3.3.1 version of gromacs.

When I solvate my protein and run grompp to generate a tpr file, it gives
me the following error

checking input for internal consistency...
calling /lib/cpp -traditional...
processing topology...
Generated 2628 of the 2628 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2628 of the 2628 1-4 parameter combinations
Cleaning up temporary file gromppXORFn5
---
Program grompp, VERSION 3.3
Source code file: toppush.c, line: 1108

Fatal error:
[ file /usr/share/gromacs/top/spc.itp, line 41 ]:
 Atom index (1) in settles out of bounds (1-0)
---

 From what it seems that the program is unable to communicate with
spc.itp file. However that should not be the case since the program
routinely does that when I run using other gromacs force fields. I have
also explicitly included the /share/gromacs/top direcly as well

I have the following lines in my preprocessor :
cpp =  /lib/cpp -traditional  ; prepocessor of the
current machine
include =  -I/usr/share/gromacs/top
define  =

Any suggestions would be much appreciated.

Many thanks

Shozeb Haider
The London School of Pharmacy

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Re: [gmx-users] problems with opls_

[TJ Piggot]

Check out ffoplsaanb.itp

Tom

--On Friday, October 26, 2007 01:05:46 -0700  huan 
[EMAIL PROTECTED] wrote:



i checked it but the what is the atomtype for opls_064
for?
thanks
--- David van der Spoel [EMAIL PROTECTED] wrote:


 huan wrote:
 i am a new user of Gromacs and i would like to
knoe
 the opls for C, =O, and -O in  RCOOR'. i tried it
many
 times but i still fail to get the proper answer..
 thanks
if you mean the atomtypes
check ffoplsaa.atp


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Re: [gmx-users] simulating hydrocarbons in water

[TJ Piggot]

Just as a note editconf will covert a pdb to a gro file

Tom

--On Wednesday, October 10, 2007 09:47:03 -0400 Adam Fraser 
[EMAIL PROTECTED] wrote:



Yes I tried this and it doesn't work for me.  I get:


Fatal error:
Library file ffG53a6.n2t not found in current dir nor in default
directories.
(You can set the directories to search with the GMXLIB path variable)

Also, doesn't x2top take in a gro file?  (not a pdb)  I wrote a script
that converts pdb to gro, and I still get the above error.

-Adam


On 10/10/07, David van der Spoel [EMAIL PROTECTED] wrote:

Adam Fraser wrote:

Hello,

I'm very new to Gromacs, and I am interested in simulating the
interactions of 2 hexadecane (C16H34) molecules in water (SPC/E
specificall).  I've spent some time experimenting with tutorials in
Gromacs, but I've found little help in non-protein simulations like this
one.

I've built topologies for hexadecane compatible with NAMD, so I figure I
should be able to do the same in Gromacs but I'm fuzzy on how to go
about doing so (what files to edit).  I was also hoping to get some
input on which forcefield would be best for this sort of system.

I'd greatly appreciate it if someone could give me some pointers on how
to get started here.

Thanks very much,
Adam


if you have a pdb file you can run x2top (3.3.2 only).





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Re: [gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose

[TJ Piggot]

Just a quick look at the ffG45a3.rtp shows that there is an entry for ADE, 
however the ADE entry is for Adenine.


For help with your problem check out:

http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database

Tom

--On Friday, September 14, 2007 14:13:55 +0100 parichita parichita 
[EMAIL PROTECTED] wrote:



Hi,

 I have facing some problem when converting .pdb file to .gro and
.top .
 I have a .pdb of alpha d-mannose (1-6) alpha d-mannose. I was using the
pdb2gmx command and 45a3 forcefield .
 Showing the fatal error:
 Atom O in residue ADE 1 not found in rtp entry with 25 atoms
  while sorting atoms
 and
Warning: 'ADMA' not found in residue topology database, trying to use
'ADE'
 Warning: 'ADMA' not found in residue topology database, trying to use
'ADE


but in  ffG45a3.rtp I could not found any ADE ...
 so I was confused ...
 Please give me some suggession.
 The format of my M6M.pdb is,

ATOM  1  C5  ADMA1   3.337   1.774  -8.944  1.00  0.00
C
 ATOM  2  O   ADMA1   4.702   1.679  -8.463  1.00  0.00
O
 ATOM  3  C1  ADMA1   5.227   0.338  -8.248  1.00  0.00
C
 ATOM  4  C2  ADMA1   4.345  -0.412  -7.222  1.00  0.00
C
 ATOM  5  O2  ADMA1   4.481   0.211  -5.965  1.00  0.00
O
 ATOM  6  C3  ADMA1   2.854  -0.372  -7.633  1.00  0.00
C
 ATOM  7  O3  ADMA1   2.063  -0.925  -6.611  1.00  0.00
O
 ATOM  8  C4  ADMA1   2.367   1.065  -7.950  1.00  0.00
C
 ATOM  9  O4  ADMA1   1.062   1.009  -8.476  1.00  0.00
O
 ATOM 10  C6  ADMA1   3.018   3.281  -9.160  1.00  0.00
C
 ATOM 11  O6  ADMA1   1.778   3.456  -9.811  1.00  0.00
O
 ATOM 12  H5  ADMA1   3.271   1.274  -9.929  1.00  0.00
H
 ATOM 13  H1  ADMA1   6.262   0.415  -7.876  1.00  0.00
H
 ATOM 14  H2  ADMA1   4.685  -1.464  -7.133  1.00  0.00
H
 ATOM 15  HO2 ADMA1   5.425   0.166  -5.725  1.00  0.00
H
 ATOM 16  H3  ADMA1   2.727  -0.987  -8.546  1.00  0.00
H
 ATOM 17  HO3 ADMA1   1.139  -0.907  -6.925  1.00  0.00
H
 ATOM 18  H4  ADMA1   2.343   1.645  -7.006  1.00  0.00
H
 ATOM 19  HO4 ADMA1   0.779   1.926  -8.640  1.00  0.00
H
 ATOM 20 1H6  ADMA1   3.805   3.735  -9.772  1.00  0.00
H
 ATOM 21 2H6  ADMA1   3.014   3.809  -8.202  1.00  0.00
H
 ATOM 22  H6  ADMA1   1.654   4.401  -9.918  1.00  0.00
H
 ATOM 23  C5  ADMA1B  5.806  -2.519 -10.516  1.00  0.00
C
 ATOM 24  O   ADMA1B  6.529  -3.735 -10.196  1.00  0.00
O
 ATOM 25  C1  ADMA1B  6.753  -4.668 -11.291  1.00  0.00
C
 ATOM 26  O1  ADMA1B  7.522  -4.046 -12.268  1.00  0.00
O
 ATOM 27  C2  ADMA1B  5.398  -5.107 -11.893  1.00  0.00
C
 ATOM 28  O2  ADMA1B  4.700  -5.870 -10.935  1.00  0.00
O
 ATOM 29  C3  ADMA1B  4.533  -3.881 -12.271  1.00  0.00
C
 ATOM 30  O3  ADMA1B  3.254  -4.305 -12.671  1.00  0.00
O
 ATOM 31  C4  ADMA1B  4.406  -2.866 -11.106  1.00  0.00
C
 ATOM 32  O4  ADMA1B  3.754  -1.706 -11.569  1.00  0.00
O
 ATOM 33  C6  ADMA1B  5.743  -1.655  -9.224  1.00  0.00
C
 ATOM 34  O6  ADMA1B  5.227  -0.368  -9.490  1.00  0.00
O
 ATOM 35  H5  ADMA1B  6.383  -1.951 -11.270  1.00  0.00
H
 ATOM 36  H1  ADMA1B  7.300  -5.545 -10.905  1.00  0.00
H
 ATOM 37  HO1 ADMA1B  7.013  -3.281 -12.602  1.00  0.00
H
 ATOM 38  H2  ADMA1B  5.572  -5.738 -12.788  1.00  0.00
H
 ATOM 39  HO2 ADMA1B  5.261  -6.638 -10.719  1.00  0.00
H
 ATOM 40  H3  ADMA1B  5.014  -3.365 -13.126  1.00  0.00
H
 ATOM 41  HO3 ADMA1B  2.756  -3.507 -12.928  1.00  0.00
H
 ATOM 42  H4  ADMA1B  3.788  -3.323 -10.307  1.00  0.00
H
 ATOM 43  HO4 ADMA1B  3.668  -1.103 -10.809  1.00  0.00
H
 ATOM 44 1H6  ADMA1B  6.749  -1.553  -8.805  1.00  0.00
H
 ATOM 45 2H6  ADMA1B  5.131  -2.153  -8.466  1.00  0.00
H
 TER


thanks in advance ..

parichita...









Parichita Mazumder
Junior Research Fellow
C/O Dr. Chaitali Mukhopadhayay
Department of Chemistry
University of Calcutta
92,A P C Road
Kolkata-79
India.


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Re: [gmx-users] about md simulation

[TJ Piggot]

Also see

http://wiki.gromacs.org/index.php/Thermostats

As you do not want to temperature couple the sodium ions independently

Tom

--On Tuesday, September 11, 2007 18:14:43 +1000 Mark Abraham 
[EMAIL PROTECTED] wrote:



amri ta wrote:

Dear colleagues,

I am simulating a phosphorylated protein embedded in waterbox.
When I try running mdrun, I get a LINCS warning.

Does this mean that I have go back to the CG-EM step and use the double
precision libs?


These should help.

http://wiki.gromacs.org/index.php/Errors#LINCS_warnings
http://wiki.gromacs.org/index.php/blowing_up
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation

Mark
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[gmx-users] Re: \\[gmx\\-users\\] The energy minimization\\.\\.\\.\\.

[TJ Piggot]

 7596 A2O ATP 800 -12.023 7.764 -6.036 1.00
41.49 O
HETATM 7597 A1C ATP 800 -11.875 6.025 -7.679 1.00
42.90 C
HETATM 7598 AN9 ATP 800 -12.608 4.832 -7.218 1.00
43.53 N
HETATM 7599 AC8 ATP 800 -12.077 3.810 -6.547 1.00
43.35 C
HETATM 7600 AN7 ATP 800 -13.023 2.904 -6.309 1.00
44.02 N
HETATM 7601 AC5 ATP 800 -14.162 3.341 -6.835 1.00
44.22 C
HETATM 7602 AC6 ATP 800 -15.461 160; 2.828 -6.899 1.00
44.02 C
HETATM 7603 AN6 ATP 800 -15.751 1.647 -6.351 1.00
43.35 N
HETATM 7604 AN1 ATP 800 -16.414 3.547 -7.525 1.00
43.25 N
HETATM 7605 AC2 ATP 800 -16.125 4.717 -8.076 1.00
43.37 C
HETATM 7606 AN3 ATP 800 -14.902 5.230 -8.032 1.00
43.76 N
HETATM 7607 AC4 ATP 800 -13.901 ; 4.571 -7.417 1.00
44.09 C --

Then i use the pdb2gmx, editconf, gromapp, (because I do EM in vacuum, so
donnot use the genbox to add water).
The .mdp file is:
---
title = Minimization
cpp = /lib/cpp
include = -I../top

integrator = steep
emtol = 1.0
nsteps = 200
nstenergy = 10
nstx tcout = 10
xtc_grps = ATP
energygrps = ATP
nstlist = 1
ns_type = simple
rlist = 1.0
coulombtype = cut-off
rcoulomb = 1.0
rvdw = 1.0
constraints = none
pbc = no
-

Would you try this ATP use your .mdp file? Thank you!

Best wishes!

Duan
;
--


Hi you need to explain in detail what steps you are doing before the
minimisation and also what parameters you are using in your .mdp file
because i have just run a minimisation of ATP (in water) to test the
topology in the GROMOS96 ff and it works fine for me, so there must  be
a problem in one of your setup steps or your simulation   parameters.



Tom







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Re: [gmx-users] The energy minimization....

[TJ Piggot]

Hi you need to explain in detail what steps you are doing before the 
minimisation and also what parameters you are using in your .mdp file 
because i have just run a minimisation of ATP (in water) to test the 
topology in the GROMOS96 ff and it works fine for me, so there must be a 
problem in one of your setup steps or your simulation parameters.


Tom

--On Friday, August 17, 2007 18:15:40 +0800 MoJie Duan 
[EMAIL PROTECTED] wrote:



Hi, Mark:
I have done the energy minimization and simulation of ATP in vacuum
individual ( Maybe you have suggested me to do this yesterday, but
actually I did not understand it, and just do this in solution).
There are following problems:
1. in the energy minimization, the potential energy is positive and in
14th step, it's potential energy is nan. But the .gro outfile of
mdrun is just the same as the original file (i.e. the .gro file before
minimization), the return messages of mdrun is (there are not any
warning):

--
Getting Loaded...
Reading file ATP.2_min.tpr, VERSION 3.3.1 (single precision)
Loaded with Money


Back Off! I just backed up ATP.2_minrun.edr to ./#ATP.2_minrun.edr.1#
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+00
   Number of steps    =  #160;    200
Step=    0, Dmax= 1.0e-02 nm, Epot=  1.06678e+05 Fmax= 3.63368e+06, atom=
26
Step=   14, Dmax= 1.2e-06 nm, Epot=  nan Fmax= 3.63313e+06,
 ^^^
atom= 26
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax  1

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Back Off! I just backed up ATP.2_minrun.gro to ./#ATP.2_minrun.gro.1#

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax  1.
Potential Energy  =  1.0667836e+05
Maximum for ce =  3.6336775e+06 on atom 26
Norm of force =    nan
___

2. in the full MD simulation, the warning coming, the messages is:


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.881911 (between atoms 27 and 28) rms nan
bonds that rotated more than 30 degrees:

 atom 1 atom 2  angle  previous, current, constraint length
 27 28   90.0    0.1610   0.3030  0.1610
Wrote pdb files with previous and current coordinates
step 2490, remaining runtime: 0 s    #160;   Writing final
coordinates.

Back Off! I just backed up ATP.2_runout.gro to ./#ATP.2_runout.gro.1#
step 2500, remaining runtime: 0 s  
__

And in the .gro file after this step, the coordinates of all atoms are
nan. So it means there are crash in the structure? Is the crash between
the atom 27 and 28? How to modify the structure file make it normal?
Thank you very much!

Duan



MoJie Duan wrote:
  So look at your structures like I said last time! I'm not her e to
  give my valuable time giving free advice in order to have it
  ignored...
 Thank you very much for your kindness and patience. Maybe sometimes my
 questions seems to be silly and boring, my knowledge about GROMACS is
 really lack, sorry.

 Actually, I really cannot understand what you said yesterday. Did you
 mean is there any difference between the atom coordinates of ATP
 before-  and after- minimization?




There would normally be some differences visible. If your topology was
badly broken, then you would usually see where it was broken.



 I found there are not any difference between
 these two structure.
 (There are also not any obvious collision between atoms of ATP when
 represent it by Rasmol)



OK, so that means your structure is in a flat area of the potential
surface defined by your topology. If the topology is sound, then you're
in business.



My first recommendation was to minimize and/or equilibrate these
structures on their own, and now I suggest doing them also in solvent.
This will help you eliminate sources of problems and guide you to
what the real problem is. Divide and conquer...



That's fine, then.



OK, so here's your problem. Work out what's breaking and why. Read the
error messages and look at the structures. Understand what each of  
your .mdp file options does.


Mark






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Re: [gmx-users] Step size too small

[TJ Piggot]

Hi,

I do not think that what Per suggests is the problem, if you look at the 
potential energy after the minimisation this value is huge (and the other 
two values are inf!). The problem is most likely with your topology. As you 
say the two molecules have been successfully minimised on their own so I 
would suggest that your problem is with either how you edit the .top file 
or the distance restraint between the molecules. For my protein that has 
more than one identical chains pdb2gmx does not recognise them as one if 
you provide different chain identifiers in the pdb file, so doing this 
should hopefully stop you having to edit the .top file.


Hope this helps

Tom

--On 17 August 2007 19:02 +0200 Per Larsson [EMAIL PROTECTED] wrote:


Hello!


Check out
http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small.2C_or_no_chan
ge_in_energy._Converged_to_machine_precision.2C_but_not_to_the_requested_
precision


Cheers
/Per



17 aug 2007 kl. 18.28 skrev Sheyore Omovie:

 Dear gmx-users,
  
 I have 2 molecules in a box, as usual pdb2gmx saw them as one. i edited
the .top file to remove the bonds created between the two molecules, I
also added a distance restraint btw the molecules. (The 2 structures have
been separately minimized). However, I get the ff message for EM run:

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax  1000
 
Double precision normally gives you higher accuracy.
 
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax  1000.
Potential Energy  =  1.0246325e+20
Maximum force =    inf on atom 1
Norm of force =    inf I would appreciate any advice on how
to fix this.
 Rgds
 John


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[gmx-users] Re: \[gmx\-users\] The energy minimization\.\.\.\. (fwd)

[TJ Piggot]

Hi

Also please keep emails on the list, it helps everyone (you getting more 
people's opinion than just mine, and people who may have a similar problem 
in the future)


Tom

 Forwarded Message 
Date: 18 August 2007 02:29 +0100
From: TJ Piggot [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Subject: Re: \[gmx\-users\] The energy minimization\.\.\.\.

Hi

I just quickly checked and your ATP pdb file works fine for me (it did have
some weird characters in it that i had to delete, not sure if this was
caused by pasting it into an email). I should point out that this pdb file
is incomplete as you are missing some hydrogen atoms (pdb2gmx should tell
you this if you modified your .rtp file correctly). See any of the GROMOS96
.rtp file ATP entries for the hydrogens you have missed that still are
included in a united atom ff.

Also your .mdp parameters work fine with your pdb file so i have no idea
what is going wrong when you try! Check you have modified the .rtp file
correctly and are supplying sensible commands to
pdb2gmx/editconf/grompp/mdrun are the last things i can suggest.

Good luck

Tom

--On 18 August 2007 08:17 +0800 MoJie Duan [EMAIL PROTECTED] wrote:


Hi,Tom:
Thank you for your reply!
Before the minimization, I just change the atoms name of ATP, so it can
coordinated to the names in ffG43b1 (the atoms name of ATP in ffG43b1
also changed, each atom have a three-letter name).

My coordinate file (.pdb) was obtained from RCSB PDB, I extracted the xyz
coordinates of ATP molecule from the a .pdb file of a protein, as
following:
___
HETATM 7577  PG  ATP   800  -4.997   4.425  -2.604  1.00
33.08   P 
HETATM 7578  O1G ATP   800  -5.685   5.603  -1.764  1.00
33.76   O 
HETATM 7579  O2G ATP   800  -3.427   4.765  -2.665  1.00 32.63  
0;    O 
HETATM 7580  O3G ATP   800  -5.273   3.100  -1.967  1.00
33.16   O 
HETATM 7581  PB  ATP   800  -5.173   3.787  -5.388  1.00
34.37   P 
HETATM 7582  O1B ATP   800  -3.985   4.318  -6.120  1.00
33.33   O 
HETATM 7583  O2B ATP   800  -5.232   2.335  -5.045  1.00
33.33   O 
HETATM 7584  O3B ATP   800  -5.529   4.675  -4.089  1.00
33.22   O 
HETATM 7585  PA  ATP   800  -7.773   3.348  -6.436  1.00
35.04   P 
HETATM 7586  O1A ATP   800  -8.260   2.720  -5.177  1.00
33.60   O 
HETATM 7587  O2A ATP   800  -7.501   2.503  -7.632  1.00
32.64   O 
HETATM 7588  O3A ATP   800  -6.483   4.274  -6.168  1.00
34.07   O 
HETATM 7589  O5' ATP   800  -8.787   4.518 0; -6.833  1.00
36.40   O 
HETATM 7590  C5' ATP   800  -8.403   5.464  -7.846  1.00
39.10   C 
HETATM 7591  C4' ATP   800  -9.604   6.315  -8.269  1.00
41.61   C 
HETATM 7592  O4' ATP   800 -10.793   5.471  -8.462  1.00
42.22   O 
HETATM 7593  C3' ATP   800  -9.937   7.303  -7.152  1.00
41.81   C 
HETATM 7594  O3' ATP   800 -10.228   8.5 59  -7.756  1.00
43.61   O 
HETATM 7595  C2' ATP   800 -11.191   6.724  -6.514  1.00
42.05   C 
HETATM 7596  O2' ATP   800 -12.023   7.764  -6.036  1.00
41.49   O 
HETATM 7597  C1' ATP   800 -11.875   6.025  -7.679  1.00
42.90   C 
HETATM 7598  N9  ATP   800 -12.608   4.832  -7.218  1.00
43.53   N 
HETATM 7599  C8  ATP   800 -12.077   3. 810  -6.547  1.00
43.35   C 
HETATM 7600  N7  ATP   800 -13.023   2.904  -6.309  1.00
44.02   N 
HETATM 7601  C5  ATP   800 -14.162   3.341  -6.835  1.00
44.22   C 
HETATM 7602  C6  ATP   800 -15.461   2.828  -6.899  1.00
44.02   C 
HETATM 7603  N6  ATP   800 -15.751   1.647  -6.351  1.00
43.35   N 
HETATM 7604  N1  ATP   800 -16.41 4   3.547  -7.525  1.00
43.25   N 
HETATM 7605  C2  ATP   800 -16.125   4.717  -8.076  1.00
43.37   C 
HETATM 7606  N3  ATP   800 -14.902   5.230  -8.032  1.00
43.76   N 
HETATM 7607  C4  ATP   800 -13.901   4.571  -7.417  1.00
44.09   C


and then changed the atoms name:


HETATM 7577  APG ATP   800  -4.997   4.425  -2.604 #160; 1.00
33.08   P 
HETATM 7578  OG1 ATP   800  -5.685   5.603  -1.764  1.00
33.76   O 
HETATM 7579  OG2 ATP   800  -3.427   4.765  -2.665  1.00
32.63   O 
HETATM 7580  OG3 ATP   800  -5.273   3.100  -1.967  1.00
33.16   O 
HETATM 7581  APB ATP   800  -5.173   3.787  -5.388  1.00
34.37   P 
HETATM 7582  OB1 ATP   800  -3.985   4.3 18  -6.120  1.00
33.33   O 
HETATM 7583  OB2 ATP   800  -5.232   2.335  -5.045  1.00
33.33   O 
HETATM 7584  OB3 ATP   800  -5.529   4.675  -4.089  1.00
33.22   O 
HETATM 7585  APA ATP   800  -7.773   3.348  -6.436  1.00
35.04   P 
HETATM 7586  OA1 ATP   800  -8.260

Re: [gmx-users] Re:

[TJ Piggot]

You should look at the ATP topology and see if the parameters you are using 
look sensible. Where did you get the topology from, did you use the united 
atom one already in the GROMOS96 ff? Also did grompp give you any warnings 
before your minimisation?


Tom

--On Thursday, August 16, 2007 01:04:55 +1000 Mark Abraham 
[EMAIL PROTECTED] wrote:



[EMAIL PROTECTED] wrote:

Dear Mark:


Please keep correspondence on the list for others to see and use.


Thanks for your help about my problem of running GROMACS energy
minimization.  I do what you suggestion,  and the protein's minization
seems to be correct, it run about 300 steps and the Ep convergent
finally, but the ATP's minimization stopped  at 14 stpes. So it means
the ATP's topology is broken? what is it means? What should  I do?


So how do you think you would be able to tell whether either or both of
these chemical structures were in a sensible energy minimum? What
observables will be useful to you here?

Mark
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Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

[TJ Piggot]

Hi,

If you are using any of the united atom GROMOS96 forcefields then there is 
already an rtp entry for ATP. Check out the .rtp files in the top folder. 
All you need to do is to have the ATP atoms in the pdb file the same as the 
atom names in the .rtp file for pdb2gmx to do all the work for you. If you 
are not using a united atom forcefield then you will have to get your 
parameters for ATP from somewhere else (or calculate them yourself - not 
easy).


Hope this helps

Tom

--On Thursday, August 09, 2007 10:03:30 +0200 Maik Goette 
[EMAIL PROTECTED] wrote:



Be aware, that you can't use the ouput with every forcefield...
Attaching the gro-file to your protein gro at the proper position (right
after the protein) and building the correct topology should do the job.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical  computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
 mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


mjduan wrote:

Yes, I found a server (ProDrg) can get the .gro and .top files of ATP
molecule.


---
Whereas one should also mention, that ATP isn't included in every
forcefield, GROMACS supports...
So probably, parameterization has to be done also.

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical  computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Mark Abraham wrote:

mjduan at smail.hust.edu.cn wrote:

Dear GROMACS users:
I want to simulate a complex composed by a protein and an ATP
molecule,  and when I use the pdb2gmx to build the topology file and
transfer  the*pdb* file to *gro* file, it said /Fatal error: Atom PG
in residue  ATP 1 not found in rtp entry with 36 atoms while sorting
atoms/, So how  can I build the *top* file and *gro* file for ATP
molecular and simulate  the protein molcular and ATP molecule
simultaneity?

By reading chapter 5 of the manual thoroughly, understanding how the rtp
files work for your force field and modifying your .pdb file and/or
force field files to work suitably.

Mark
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Re: [gmx-users] Implicit solvent simulation

[TJ Piggot]

Hi,

Just to let people know in case they are unaware there is a paper where 
implicit solvent models have been implemented in GROMACS, the paper can be 
found using the following link:


http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmedpubmedid=15814616

Tom

--On Wednesday, July 18, 2007 15:39:43 +0200 David van der Spoel 
[EMAIL PROTECTED] wrote:



SeungPyo Hong wrote:

Thank you for your kind reply, Stephane.
Anyhow it is a little disappointing that Generalized-Born is not
implemented in Gromacs.



I've put it on the development TODO list (feel free to volunteer)

http://wiki.gromacs.org/index.php/Implicit_Solvent

The reason it is not there is because none of the developers has
considered it worthwhile.

--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] Implicit solvent simulation

[TJ Piggot]

If you REALLY want implicit solvent then i suggest you contact the authors 
and ask them about it, however i (like most others i think) have never 
needed to use implicit solvent.


Tom

--On Wednesday, July 18, 2007 16:17:01 +0200 Ran Friedman 
[EMAIL PROTECTED] wrote:



Dear Tom,

The paper is available and was mentioned in the list. The model,
however, isn't available AFAIK.

Ran.

TJ Piggot wrote:

Hi,

Just to let people know in case they are unaware there is a paper
where implicit solvent models have been implemented in GROMACS, the
paper can be found using the following link:

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmedpubmedid
=15814616


Tom

--On Wednesday, July 18, 2007 15:39:43 +0200 David van der Spoel
[EMAIL PROTECTED] wrote:


SeungPyo Hong wrote:

Thank you for your kind reply, Stephane.
Anyhow it is a little disappointing that Generalized-Born is not
implemented in Gromacs.



I've put it on the development TODO list (feel free to volunteer)

http://wiki.gromacs.org/index.php/Implicit_Solvent

The reason it is not there is because none of the developers has
considered it worthwhile.

--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax:
+4618511755.
[EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
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--
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Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
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Tel. +41-44-6355593
Email: [EMAIL PROTECTED]
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Re: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units

[TJ Piggot]

If i understand correctly then rlist is the short range cutoff inside which 
the forces on the atoms are calculated every step (and the neighbour list is

updated every nstlist steps).
If you specify a value of rvdw or rcoulomb larger than rlist then the 
forces on the atoms between rlist and rvdw/rcoulomb are re-calculated only 
every
nstlist steps (and again the neighbour list is updated every nstlist 
steps). However it does not make sense to do this for rcoulomb when using 
PME because if you did this then forces inside rlist and outside rcoulomb
would be updated every step but for outside rlist and inside rcoulomb only 
updated every nstlist steps, so for PME rcoulomb should equal rlist.


I think this is correct but i am sure someone will tell me if it is not.

Tom

--On Monday, July 16, 2007 06:56:41 -0400 Frankie Montenegro 
[EMAIL PROTECTED] wrote:



Hi guys,

My first question is with regards to the size relationship
between rlist and rvdw/rcoulomb, and consequently the
meaning of rlist.

I found an excellent question on this exact same subject
 posted couple of years ago, but I couldn't find the answer to
 it. I copy parts of the question here, and I would greatly appreciate
some comments. It's rather long, so I tried to cut
 and paste parts of it that are relevant to me.


Quote:

[gmx-users] again, rlist vs rvdw vs rcoulomb and something about energy
groups
m b mic0404 at yahoo.com
Fri Jul 25 04:32:00 CEST 2003


dear all,

I do MD simulations using a cutoff for
both VdW and Coulomb interactions.
I am rather confused about the
parameters used in the input file.
(rlist, rvdw, rcoulomb)

cut--

Normally I would assume that if one uses
a neighbour list there are (at least) two cutoffs:
One for a sphere around each atom with ALL
(and only) the atoms in this sphere considered when
calculating the energy and the forces on
the primary atom at EACH time step (rvdw,
rcoulomb ?).
A second (larger) cutoff that is used when
calculating the neighbour-list at intervals
of each 10 (or so) time steps (rlist ?)
were of course rlist  rvdw and rcoulomb.

If one uses a switched potential there
is a third cutoff (the onset of the switching
function) that would be shorter than
rvdw and rcoulomb.

this implies: rlist  rvdw,rcoulomb  r*_switch
... in contrast to (part of) the manual, and the
errormsg given by the code.

--cut--

In my calculations I now let
rlist  rvdw, rcoulomb, to evade
the error message that Gromacs gives me
otherwise, but if what I wrote above is true
then the physical implications would
be a bit worrying ...
and if I have rlist = rvdw, rcoulomb
would that not mean that the neighbour list
has to be re-calculated at each time-step
to get consistant results ?

So the question is: is what I wrote above
correct or not ? and if not, what is the
precise meaning of these parameters (rlist,
rvdw, etc)


End of Quote.


My second question
I am trying to minimize a model binary Lennard-Jones system.
 It is a cubic box, side length 5 sigmas (so, the size is in
 reduced units, sigma=1).I have two atom types, so I followed
 the manual and set sigma_ii = epsilon_ii = 1 for one atom type.
 I set rlist=1, but grompp_d complaines that

 ERROR: The cut-off length is longer than half
  the shortest box vector or longer than the
  smallest box diagonal element. Increase the
  box size or decrease rlist.

Now, it seems to me that, if sigma_ii = 1, all lengths values in the
mdp file (such as rlist) will be in units of sigma. Am I right
 here? r*=r/sigma=r/1=r, right? If so, why is grompp complaining about
the size which is less then a quarter of the
 box? (At first I thought it is complaining about rlist being too
 small.)

So, in conclusion, I either don't understand:

A) meaning of the size of rlist,

B) conversion to reduced units,

C) quite possibly both.

Here is my potential, if that can be of any help.

PE_ij=sigma_ij^6 * [ 16.0* epsilon_ij / R_ij^6
 - 12.0 * epsilon_ij * r_ij^2 / R_ij^8
 - 4.0 * epsilon_ij / r_ij^6 ]
+sigma_ij^12 * [-28.0 * epsilon_ij / R_ij^12
+24.0*epsilon_ij * r_ij ^2/ R_ij^14
+ 4.0 * epsilon_ij  / r_ij^12 ]

where R_ij= const * sigma_ij
is the cutoff for each of the three interactions.

Thanks for your help,
Frankie
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Re: [gmx-users] which tool to use a measure a user-defined angle in a traj

[TJ Piggot]

Hi,

I would use g_bundle with the -z option.

Tom

--On 14 July 2007 10:51 -0400 [EMAIL PROTECTED] wrote:


For instance, I want to measure the angle defined by a carbonyl
vector (a vector going through a C=O bond) in my molecule and the
z-axis of the simulation box.


Not sure if that tool exists. You could, however, do this:
1) use make_ndx to make an index group of only the two atoms of interest
2) trjconv -f entire.xtc -o two_atoms.gro
3) write a simple script to parse the output .gro trajectory file in
order to obtain the angle to the z axis based on cos(theta)=(z2-z1)/r
therefore theta=arccos[(z2-z1)/r] where the angle is defined to the
negative z direction. If you used constraints for that bond then it  will
be especially simple, otherwise you will need good old pythagoras  to get
r.
Note1) If you've got lots of angles that you want to average over, the
process is the same but with more book-keeping.
Note2) You could also try modifying template.c

Good luck.

PS: if you do write a script, please post it back to the list.

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Re: [gmx-users] g_bundle!

[TJ Piggot]

use the program make_ndx or just edit the .ndx file using a text editor

Tom

--On 21 June 2007 11:03 -0700 priyanka srivastava [EMAIL PROTECTED] 
wrote:



Does this mean defining my own .ndx file and not using
the default one?

If yes, can you please drop some hints of how to make
the .ndx file for this purpose.

thanks and regards,
Pri...


--- Alan Dodd [EMAIL PROTECTED] wrote:


I've used g_bundle a lot for just this sort of
thing.  You need to define the top and bottom of the
helix as seperate groups, and define them *very*
carefully - it does make a difference how you do it,
presumably because g_bundle just plots the axis
between the COM of both groups?  I usually define as
close to 1 complete turn of the backbone of the
helix at each end as possible.
Your output is not surprising, given what you've
asked the program for - the axis between two points
that precisely overlap ;-)

- Original Message 
From: priyanka srivastava [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Sent: Wednesday, June 20, 2007 3:27:42 PM
Subject: [gmx-users] g_bundle!


Dear All,

I want to calculate tilt angle of a peptide inserted
inside the lipid bilayer (i.e. angle between the
helical axis and bilayer normal). From previous
posts
I got an idea that g_bundle wud solve my problem.

I am issuing the following on the command line:

g_bundle -f test.xtc -s test.tpr -na 2 -z -tu ps

This asks me to Select a group of top and a group
of
bottom atoms

Group 0 (  System) has 12877 elements
Group 1 ( Protein) has   102 elements
Group 2 (   Protein-H) has79 elements
Group 3 ( C-alpha) has10 elements
Group 4 (Backbone) has31 elements
Group 5 (   MainChain) has41 elements
Group 6 (MainChain+Cb) has49 elements
Group 7 ( MainChain+H) has54 elements
Group 8 (   SideChain) has48 elements
Group 9 ( SideChain-H) has38 elements
Group10 ( Prot-Masses) has   102 elements

when I chose 1 and 1 it gives all angles as 90,
which is wrong and bun_tiltr is reported as nan.
The
manual says that the program reads two index groups
and divides both of them in -na parts.
I am a lil confused! what should be my choice here?

regards,
Pri...







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Re: [gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files

[TJ Piggot]

Hi,

I think that the terminal oxygen atoms should not be named OXT for the 
amber forcefields but rather OC1 and OC2. To check this look in the top 
folder at the ffamberXX.rtp file.


Hope this helps

Tom

--On Tuesday, June 12, 2007 15:30 -0400 Robert Johnson 
[EMAIL PROTECTED] wrote:



Hello everyone,
I'm attempting to run a simulation of a protein that contains an atom
named OXT (for the terminal oxygen atom). We are using the amber force
field and have already successfully built a topology for the protein.
However, when running Grompp we consistently receive the following
error message:

Warning: atom names in topology.top and coordinates.pdb don't match (OXT
- O2)

However, checking the actual files reveals that the atoms were
initially named consistently. It seems that whenever we run various
Gromacs programs (such as grompp or editconf), the OXT atom name is
changed to O2. In other words, topology.top and coordinates.pdb both
have the atom correctly named as OXT. It seems that Gromacs wants to
substitute a 2 for the XT.

Does anyone know why Gromacs does this? Is this due to a bug in the
code or is there some environment variable that defines XT=2?

Thanks,
Bob Johnson
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Re: [gmx-users] protein-DNA simulation with Amber port

[TJ Piggot]

Figured it out was just being a bit slow. I hadn't include an #ifdef 
_FF_AMBER statement in spce.itp or spc.itp


Thanks Erik and Mark

Tom

--On Friday, June 01, 2007 23:35:22 +1000 Mark Abraham 
[EMAIL PROTECTED] wrote:



TJ Piggot wrote:

Hi

I have just checked again by trying to set up a run again using spc/e
with amber03. I still get this same error. I am sure the order in the [
molecules ] section is correct, and it is the same order as in the .top
file with tip3p or tip4p which both work fine. The only difference
between the setup's is the -water option given to pdb2gmx and the -cs
option in genbox


How do the contents of the water .itp files differ?

Mark
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Re: [gmx-users] pdb2gmx error

[TJ Piggot]

You do not want to use the ffgmx forcefield. For simulating DNA and protein 
i would use the amber force field. For more info on the ffamber ports see:


http://folding.stanford.edu/ffamber/

Tom

--On Wednesday, May 30, 2007 04:17:26 -0700 Alaguraj Veluchamy 
[EMAIL PROTECTED] wrote:



Dear gmx-users,
I am trying to run a simulation of a pdb with DNA molecule.
I have give gromacs force fied and the error i found was,

There are 5 chains and 0 blocks of water and 372 residues with 3341 atoms

  chain  #res #atoms
  1 'A'   162   1245
  2 'B'   162   1245
  3 'C'21417
  4 'D'21428
  5 'E' 6  6

All occupancies are one
Opening library file /usr/local/gromacs/share/top/ffgmx.atp
Atomtype 52
Reading residue database... (ffgmx)
Opening library file ffgmx.rtp
Residue 50Fatal error: Atom type OWT4 (residue HO4) not found in atomtype
database

Although there are posts to use the PRODRG, but it gives error that more
than 300 atoms cannot be processed.
i am able to do simulation the pdb without DNA.
but with protein-dna complex it shows the above error.
what may be the solution ?
Regards,
A.Raj

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Re: [gmx-users] Question about MD simulation

[TJ Piggot]

You want to name the atoms according to the atom types in ffamberXX.rtp 
file. For an example of this for DNA see the dickerson.pdb provided in the 
README directory of the ffamber port or this pdb can be downloaded on its 
own from:


http://folding.stanford.edu/ffamber/

Tom

--On 30 May 2007 13:05 -0700 bo yang [EMAIL PROTECTED] wrote:


Dear gromacs users,

I have a quetion regarding using amber forcefield in gromacs.
I did the DNA and water interaction simulation. After the energy
minimization, the
original helix-structured DNA becomes two fragments. At this stage,
I assume that the simulation process is correct.
I used exactly same energy minimization em.mdp file for my nanotube-water
simulation. Since I am using amber forcefield, I changed the name of all
atoms (C, H) of my nanotube according to the name used in ffamberXX.itp.
For example, C is renamed as amberXX_42.
During the energy minimization, I got warning messages as:
WARNING: Writing out atom name (amber) longer than 4 characters to .pdb
file
Also, the EM result is Segmentation Fault.

Can anyone give me some suggstions or hints how to solve the problem?
Is there any other ways to rename those atoms (either in NT or amber
files)?

Thank you very much!
Bo




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Re: [gmx-users] Problems using grompp and amber force field

[TJ Piggot]

Hi,

With regards to the versions you are correct, ffamber_v3.3.1 is for use 
with Gromacs 3.3.1. As for the error i would suggest you do what Mark says 
and make sure all your inclusions are correct.  If you still can't find the 
problem then you need to post some of your .top file so we can have a look 
at it


Tom

--On 08 May 2007 10:53 +1000 Mark Abraham [EMAIL PROTECTED] wrote:


root wrote:

Dear GROMACS user:

Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of
http://folding.stanford.edu and now I understand your comments.
We tried with cpp = /lib/cpp -traditional in the mdp file. The warning
desapears, but the error messages is similar.
(Fatal error:

Atoms in the .top are not numbered consecutively from 1

---

We tested the dick.top file, and we verified that the atoms

are numbered

consecutively from 1 to 758.)


Have you inspected the #included files as well? The way cpp works, any
file #included is literally dropped into its parent file, so if you had
something wrong in such an #inclusion you'd need to fix that.

Mark
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Re: [gmx-users] Inconsistent shifts using multiple bonds type 6

[TJ Piggot]

Hi Berk,

Thanks for your reply. Yes the latter is the case in my system so i will 
use pbc=full or remove these 'bonds' that i know will be greater than half 
of a box dimension


Thanks again

Tom

--On Tuesday, March 06, 2007 10:52:52 +0100 Berk Hess [EMAIL PROTECTED] 
wrote:







From: TJ Piggot [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] Inconsistent shifts using multiple bonds type 6
Date: Tue, 06 Mar 2007 00:22:00 +

Hi Mark thanks for your reply,

I'm not sure the problem is that these restraints are inappropriate, but
the problem might be the sheer number. For example if i restrain a
fairly  large number of atom distances (say 100 Calpha distances) to the
same  length they are in the structure after minimisation and position
restrained  MD then mdrun still crashes, even if i use a very weak force
for the  restraint.

I have also been playing round trying to fix the problem and have
noticed  from the mailing list that inconsistent shifts are seen when
people are  using infinite systems and have not set pbc=full. I know i
am not using the  kind of system but setting pbc=full does not result
these problems that i  see when i use pbc=xyz. Is pbc=full reasonable to
use for production runs  and does anyone know roughly how much slower it
is (time is quite important  as i have a large system)

Thanks again

Tom


Inconsistent shift should only occur with infinite molecules,
or when distances between atoms connected by bonded
interactions exceed half a box dimension.
Is the latter the case for your system?

You can safely use pbc=full for production runs (I only noticed
recently this option is missing in the mdp option manual).
The performance difference should be a few percent.

Berk.

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Re: [gmx-users] Inconsistent shifts using multiple bonds type 6

[TJ Piggot]

Hi Mark thanks for your reply,

I'm not sure the problem is that these restraints are inappropriate, but 
the problem might be the sheer number. For example if i restrain a fairly 
large number of atom distances (say 100 Calpha distances) to the same 
length they are in the structure after minimisation and position restrained 
MD then mdrun still crashes, even if i use a very weak force for the 
restraint.


I have also been playing round trying to fix the problem and have noticed 
from the mailing list that inconsistent shifts are seen when people are 
using infinite systems and have not set pbc=full. I know i am not using the 
kind of system but setting pbc=full does not result these problems that i 
see when i use pbc=xyz. Is pbc=full reasonable to use for production runs 
and does anyone know roughly how much slower it is (time is quite important 
as i have a large system)


Thanks again

Tom

--On 06 March 2007 09:57 +1100 Mark Abraham [EMAIL PROTECTED] wrote:


Hello all,

I am trying to apply a set of harmonic distance restraints between pairs
of
protein atoms in my system, which is protein/ligand/water/ions in a
periodic box.

The way i am doing this is to use the bond type 6 and to add these bonds
at
the end of the [bonds] section in my topology file, after the system has
been energy minimised and i have performed position restrained MD,
without these harmonic distance restraints.

I can then run it through grompp with no problems and start mdrun. If i
only have a few (ie less than about 30) harmonic distance restraints then
the simulation if fine and runs happily. However if i increase the number
of restraints then mdrun crashes due to lincs warnings and it also says
that the are inconsistent shifts, (the number of inconsistent shifts
varies
depending on which atoms i choose to restrain and also the number of
atoms chosen) a warning not seen with less harmonic distance restraints.


Why do you need more harmonic restraints?


I should also say that i have run this system without these harmonic
restraints without problems for tens of nanoseconds already. Also this
problem can be repeated if i try to use the [distance_restraints] however
it requires less restraints to get the inconsistent shift warning (and
lincs problems) this way.

If anyone can give me an idea of what is causing this problem it would be
warmly appreciated, or even just how to detect which of the harmonic
distance restraints will cause the problem before i run mdrun so i can
replace the problem 'bonds' in the topology file.


You can't tell a priori, but if you watch the trajectory you should start
to get an idea what is breaking where and this will narrow down the number
of inappropriate restraints.

Mark

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Re: [gmx-users] opls parameters

[TJ Piggot]

Hi,

I don't see why it doesn't all work, can you not just use the 
ffoplsaanb.itp file to map the opls_xxx names to the ones used in 
ffoplsbon.itp?


Cheers

Tom

--On 03 December 2006 08:23 +1100 Mark Abraham [EMAIL PROTECTED] 
wrote:



Komath Damodaran wrote:

Hi All,

I am trying to build the itp file for a molecule. I would like to use
the opls force field. The ffoplsaa.atp contains the atom types as
opls_xxx. But the ffoplsbon.itp which contains the bond-angle-dihedral
parameters does not use the opls_xxx convention. Is there a way to
identify the bond/angle/torsion parameters of a set of opls_xxx atoms?


There ought to be a mapping somewhere... ffoplsaanb.itp has opls_xxx and
then some other stuff, but it doesn't all work... weird.

Mark
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[gmx-users] OPLS-AA Charge Calculation

[TJ Piggot]

Hi all,

I am trying to calculate partial charges of a ligand for the OPLS-AA/L 
forcefield. I have searched the mailing lists and literature and would like 
to confirm that the approach i am going to take is a sensible and accurate 
one.


Firstly i take an all atom structure of the ligand and minimise in 
gaussian03 using the RHF method and 6-31G* basis set (is this a suitable 
level of theory for my charged ligand of 43 atoms?).


Then i calculate the electrostatic potential using the CHelpG method and 
output it on a grid.


Then use a two stage RESP fitting to calculate the charges.

Thanks for any input you have on this approach

Tom Piggot

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Re: [gmx-users] pdb2gmx error, How to generate the gro and top file for a small molecular?

[TJ Piggot]

By hand for the topology, check chapter five of the manual.

For the gro file use editconf to convert the pdb

Hope that helps

Tom

--On Tuesday, June 13, 2006 17:40:41 +0800 SUN, Jian 
[EMAIL PROTECTED] wrote:




Dear all,

I am doing the simulation of a protein with a small molecular in its
active site.
But unfortunately, pdb2gmx cannot generate the gro and top file for the
small molecualr?
I am using the oplsaa force field, who can tell me how to generate the
gro and top files?

Thanks a lot
Jian




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