Re: [gmx-users] GPU + surface

2013-08-09 Thread Lucio Montero 
Hello. ¿Have you removed periodicity?. Because you may only be seeing 
traversal of water molecules among copies of the periodic system.

Lucio Montero
Ph. D. student
Instituto de Biotecnologia, UNAM
Mexico


El 08/08/13 07:39, Ondrej Kroutil escribió:

Dear GMX users.
   I have done simulation of ions and water near quartz surface
(ClayFF) using GPU (GTX580) and Gromacs (4.6.1, single precision, 64
bit, SSE4.1, fftw-3.3.3) and have observed strange behavior of water
and ions. Its NVT simulation with freezed surface atoms (see .mdp
below) and negative charge on surface (deprotonated silanols), system
is overall neutral. I used same mdp for normal CPU simulation and GPU
simulation, and just added -testverlet option for GPU simulation.
   In CPU simulation ions and water behaved as expected (see
http://i1315.photobucket.com/albums/t587/Andrew_Twister/cpu-simul_zpscf784b46.png)
, but in GPU simulation there was a visible flow of ions toward image
of lower surface and all water molecules were oriented with hydrogens
facing downward and oxygens oriented upwards (see
http://i1315.photobucket.com/albums/t587/Andrew_Twister/gpu-simul_zps2c160ea6.png).
It looks like there was an applied electric field but it is not.
   Do you think there is a problem in initial setup of parameters in
mdp file? Or maybe problem of freezing groups? With no freeze
situation is better, but there is still visible flow and pairing of
same ions (see 
http://i1315.photobucket.com/albums/t587/Andrew_Twister/gpu-no_freeze_zps72ef3938.png).
   It look as electrostatics problem. Do you have any hints, please?
And sorry if I missed similar topic in mailing list, but I couldn't
find anything similar.

   Ondrej Kroutil

integrator   =  md
dt   =  0.001
nsteps   =  10
comm_mode=  linear
nstcomm  =  1000
nstxout  =  0
nstxtcout=  1000
nstvout  =  0
nstfout  =  0
nstlog   =  1000
xtc_precision=  1
nstlist  =  10
ns_type  =  grid
rlist=  1.2
coulombtype  =  PME
rcoulomb =  1.2
rvdw =  1.2
constraints  =  hbonds
constraint_algorithm =  lincs
lincs_iter   =  1
fourierspacing   =  0.1
pme_order   =  4
ewald_rtol  =  1e-5
ewald_geometry  =  3dc
optimize_fft=  yes
; Nose-Hoover temperature coupling
Tcoupl =  nose-hoover
tau_t  =  1
tc_grps=  system
ref_t  =  298.15
; No Pressure
; Pcoupl =   Parrinello-Rahman
pcoupltype  =  semiisotropic
tau_p   =  1.0
compressibility =  0 4.6e-5
ref_p   =  0 1.0
; OTHER
periodic_molecules  =  no
pbc =  xyz
;energygrps = SOL SOH
freezegrps  = BULK
freezedim   = Y Y Y
gen_vel = yes
gen_temp= 298.15
gen_seed= -1



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Re: [gmx-users] Atomtype CMET not found

2010-11-16 Thread Lucio Montero 
¿Did you change also the name of the “residue” (from 1MeOH to 1CH3OH (that is 
the “residue” name appearing in the RTP file))?
Best regards
Lucio

From: Mina Madah 
Sent: Tuesday, November 16, 2010 6:00 AM
To: gmx-users@gromacs.org 
Subject: [gmx-users] Atomtype CMET not found

  Dear all

  I am using gromacs 4.5.1. I am running gromacs examples (methanol). when 
I use grompp -v, I encounter a fatal error: Atomtype CMET not found. I 
understand gromacs use ffG43a1. In rtp file of this forcefield there is: 

  [ CH3OH ]
  [ atoms ]
  Omet  OMet-0.57400 0
  HMet H 0.39800 0
  CMet  CMet 0.17600 0

  and in atp file of this forcefield there is:

  CMet  15.035   ; CH3-group in methanol (solvent)

  conf.gro for methanol is as follows:
  1MeOH   Me11   1.090   1.374   0.894 -0.2255  0.0272 -0.0476
  1MeOHO22   1.205   1.439   0.863  0.3805 -0.9040  0.2153
  1MeOHH33   1.174   1.533   0.851  0.7376 -0.5702  1.7130

  I changed above conf.gro file as that be consistent with atp and rtp file.

  but when I use grommp -v again with new gro file: 

  fatal error:
  Atomtype CMET not found

  is my manner true?
  any help will highly appreciated about this problem.


 





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Re: [gmx-users] simulation of protein in presence of ATP

2009-06-26 Thread Lucio Montero 
Independently of your ATP position, your system may explode or show 
LINCS warnings if you use pressure and temperature coupling. I had these 
problem, and corrected it removing the pressure coupling. Pressure 
coupling will let your system expand in response to the heat, and if the 
positions are restrained, it`s going to develop a big force that makes 
your system explode, as happens in real life.


nikhil damle escribió:

Hi

When i subjected the complex to EM, it gave following warning:
"1-4 interaction between 3063 and 3068 at distance 1.436 which is 
larger than the 1-4 table size 1.000 nm. These are ignored for the 
rest of the simulation. This usually means your system is exploding,"


These atoms are oxygens of 2 phosphate grps ofATP. Later if i 
continue, with SD it converges with less precision. so i applied CG. 
It converged. But when I carry out position-restrained dynamics, it 
gave # of LINCS warnings in both cases. Does this mean EM is not done 
properly ? How should I address this ?


Regards,
Nikhil


*From:* Mark Abraham 
*To:* Discussion list for GROMACS users 
*Sent:* Tuesday, 23 June, 2009 9:10:15 PM
*Subject:* Re: [gmx-users] simulation of protein in presence of ATP

nikhil damle wrote:
> OK till here done ! the pdb file generated for EM should have ATP 
molecule @proper position as input .top file has the ATP.itp included. 
It did not have. If I do -ci it would randomly replace the solvent. I 
want ATP @ its proper location. how do i do this ?


Like I implied several emails ago, you should order the [molecules] 
entries according to the coordinate file, as normal.


Mark
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--
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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Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRGassigned ones

2009-04-19 Thread Lucio Montero 
How can you calculate computationally charges for molecules containing 
phosphates?




--
From: "Ran Friedman, Biochemisches Inst." 
Sent: Friday, March 27, 2009 2:35 PM
To: ; "Discussion list for GROMACS users"

Subject: Re: [gmx-users] HF/6-31G** ESP derived charges to replace
PRODRGassignedones


Dear Josmar,

You haven't written which force field you plan to use. For OPLS and
AMBER QM-based optimisation should be fine. In Gromos, the FF was
developed with the aim of reproducing experimental results and I'm not
sure if you can find a better solution than examining other residues
with the same chemical moieties or use the same approach as reported
in the relevant manuscripts. Some software packages can also be used -
these are mostly proprietary and not so easy to use.

Once you derive the parameters, it's a good idea to make some test
runs of the ligands and see if they behave as expected before you
actually run a simulation with the protein. For example, if a
conjugate ring system isn't planar something may be wrong in the 
setting.


There's no easy solution - this is why it's considered an advanced
topic. It is, however, very important. I've encountered a ligand that
leaves its binding site during a simulation due to wrong parameters
(in this case, the protonation of a protein side chain - FEBS  581,
Pages 4120-4124, 2007).

Hope that helped,
Ran

On Fri, 27 Mar 2009 12:22:01 -0700 (PDT)
 "Josmar R. da Rocha"  wrote:

Dear users,

I have been reading some posts about using externally computed
charges to replace Prodrg charges at ligand topology files. Many
users commented on the low trustability given to Prodrg charges (e.g
http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ;
http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ).
Dr. Verli pointed out the use of semi-empirical methods such as RM1
in cases not involving simulations with sulphate or phosphate groups
(what is not my case) and the use of QM methods with the 6-31G**
basis set, for example, to obtain robust charges
(http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On
the other hand Dr. Mobley defined as a "a bad idea to compute charges
for an all-atom case using QM and then try to convert these to a
united atom force field". Other users advice that the best charges
are that compatible with the force field parametrization
(http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ;
http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html),
usually pointing to
http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman
suggested that "to calculate the electrostatic potential over the
whole molecule, and fit the atomic charges so that they reproduce
this potential" in order to make it less sensitive to small changes
in the geometry of the molecule may give good results
(http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html).
Dr. Lemkul stressed the need for charges refinement to reproduce
experimentally-observed behavior while trying to use QM charges with
Gromos ff. since "Parameterization under Gromos usually involves
empirical derivation of physical parameters, and free energy
calculations using thermodynamic integration". Few examples of
protein-ligand studies using Gromacs and Gromos96 ff that I have
access (from literature) seem to treat it as "take it for granted"
issue (any reference with a more detailed description would be
welcome :-)). Despite reading on this topic I could not compile all
the information in a clear and objective way (may be because I'm in
the wrong track). Let ask you some question that I find would help me
to make my ideas more clear:


1-am I overestimating the importance of ligand charges in such a
simple study of protein-small molecule (containg charged Phosphate
groups) complex? or

1.1-The only way to test for this is doing many different simulation
on the same system using different type of computed charges to see
what happen?

2-How could I try to choose a method to obtain reasonable charges
based on the reproduction of experimentally-observed behavior if I do
not have experimental data for my system?

3-I also would like to know from users dealing with protein-ligand
interactions studies what do you consider a good approach to address
this problem?

Based on what I read I'd have a tendency to use HF/6-31G** ESP
derived charges (with necessary changes as to make it united-atom
charges and scaling that to a integer number for each group). Please,
let me know if that strategy would be as good as a disaster! Thank
you very much for the attention.


Josmar Rocha



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Re: [gmx-users] Pressure Coupling Problem

2009-04-13 Thread Lucio Montero 
I don't know the conditions you use with your system, but sometimes there are 
problems when you use pressure coupling in a system with positionally 
restrained or fixed atoms.
Cheers.
 Lucio.


From: Joe Joe 
Sent: Friday, April 10, 2009 12:12 PM
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Pressure Coupling Problem


I finally figured it out. I went through every parameter step by step and it 
turns our I had epsilon-r set to 80. Not sure why I had that. Wish gromacs 
would have given me a warning (hint hint). That explains why my P.E. was 10^-5 
instead of 10^-6. Thanks everyone for trying!!!. Sometime the most obvious 
mistake takes some time to figure out. 


Cheers,



Ilya




On Fri, Apr 10, 2009 at 8:05 AM,  wrote:

  Alright, sorry that I wasn't able to help. I'm confused by some apparent 
contradictions in your posts and I'm not sure that I'm going to be useful to 
you here.

  Quoting http://www.gromacs.org/pipermail/gmx-users/2009-April/041173.html: 
"No matter how much minimization I do the volume of the box expands when run it 
using berendsen pressure coupling with a tau_p -f .1."

  Quoting http://www.gromacs.org/pipermail/gmx-users/2009-April/041159.html: 
"So I got my small water box (800 waters) to behave stably with pressure 
coupling after more minimization ..."

  Good luck.
  Chris.

  -- original message --


  Nope not an A/nm problem.
  As a simple test I take spc.gro from share/top.
  I reconfigure the box (i.e. editconf -f spc.gro -d 1.0 -c -bt cubic -o
  water_center.

  I then solvate with genbox, minimize and run using the mdp file I provided
  earlier.

  No matter how much minimization I do the volume of the box expands when run
  it using berendsen pressure coupling with a tau_p -f .1.

  Ilya


  On Thu, Apr 9, 2009 at 11:22 AM, Chris Neale wrote:

  [Hide Quoted Text]
  So your problem with the small water box was solved simply by adding more
  minimization? I then suspect that all of your problems are simply related to
  a bad starting structure -- and by the sound of it is really is very bad.
  Are you sure that you don't have an angstrom / nm problem here?

  Chris.

  -- original message --

  So I got my small water box (800 waters) to behave stably with pressure
  coupling after more minimization but I still can't get my large system to
  work with pressure coupling. I tried minimizing but I can never get the
  Fmax to be less 102, which is pretty normal for protein/water simulations of
  large proteins, at least from my experience.  I have since run 400 ps NVT
  as ...

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Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRGassigned ones

2009-04-03 Thread Lucio Montero 

I was thinking that's not such a problem switching tha OPLS-AA, since most
of the atoms in my system are from water, that will remain being spc.

--
From: "Lucio Ricardo Montero Valenzuela" 
Sent: Wednesday, April 01, 2009 12:59 AM
To: "Discussion list for GROMACS users" 
Subject: Re: [gmx-users] HF/6-31G** ESP derived charges to replace
PRODRGassigned ones


I wanted the OPLS-UA because my system is large (3 proteins with 2 organic
molecules, in water), and, if the G43a1 forcefield gives me a MD speed of
70
ps/day, an all atom model will result much slower. So what else can I do
to
speed up my MD, to get results in 1-3 months?.
Mensaje citado por David van der Spoel :


Lucio Ricardo Montero Valenzuela wrote:
> So it 's better to switch to the OPLS forcefield if I want to compute
> the
> charges?.
> How can I implement the OPLS-UA if my gromacs (version 3.3) only
> includes
the
> OPLS-AA?

We don't support United atom OPLS because Jorgensen himself does not use
it anymore. That if something should indicate for you that the united
atom force field has been superseded by the all-atom. Jorgensen himself
uses OPLS-AA with TIP4P, so this is probably the best recommendation.
Most important, if you chose to use another combination, you basically
have to prove that this "works" as well (whatever that means...)

> Mensaje citado por "Justin A. Lemkul" :
>
>>
>> Lucio Montero wrote:
>>> How about MOPAC to calculate the charges for 3-methyladenine (this
>>> molecule has a charge +1) for using the G43a1 force field?.
>>>
>>>
>> That may not be a bad place to start, but any parameters applied to a
Gromos
>> molecule have to reproduce condensed phase thermodynamic observables.
>> Empirical
>> fitting of the initial parameters may be required.  Refer to the
>> primary
>> literature.  The reference for the 53a5 and 53a6 parameter sets are
published
>> in
>> JCC, which may provide you with some useful information.
>>
>> -Justin
>>
>>> --
>>> From: "Ran Friedman, Biochemisches Inst." 
>>> Sent: Friday, March 27, 2009 2:35 PM
>>> To: ; "Discussion list for GROMACS users"
>>> 
>>> Subject: Re: [gmx-users] HF/6-31G** ESP derived charges to replace
>>> PRODRGassignedones
>>>
>>>> Dear Josmar,
>>>>
>>>> You haven't written which force field you plan to use. For OPLS and
>>>> AMBER QM-based optimisation should be fine. In Gromos, the FF was
>>>> developed with the aim of reproducing experimental results and I'm
>>>> not
>>>> sure if you can find a better solution than examining other residues
>>>> with the same chemical moieties or use the same approach as reported
>>>> in the relevant manuscripts. Some software packages can also be
>>>> used -
>>>> these are mostly proprietary and not so easy to use.
>>>>
>>>> Once you derive the parameters, it's a good idea to make some test
>>>> runs of the ligands and see if they behave as expected before you
>>>> actually run a simulation with the protein. For example, if a
>>>> conjugate ring system isn't planar something may be wrong in the
setting.
>>>>
>>>> There's no easy solution - this is why it's considered an advanced
>>>> topic. It is, however, very important. I've encountered a ligand
>>>> that
>>>> leaves its binding site during a simulation due to wrong parameters
>>>> (in this case, the protonation of a protein side chain - FEBS  581,
>>>> Pages 4120-4124, 2007).
>>>>
>>>> Hope that helped,
>>>> Ran
>>>>
>>>> On Fri, 27 Mar 2009 12:22:01 -0700 (PDT)
>>>>  "Josmar R. da Rocha"  wrote:
>>>>> Dear users,
>>>>>
>>>>> I have been reading some posts about using externally computed
>>>>> charges to replace Prodrg charges at ligand topology files. Many
>>>>> users commented on the low trustability given to Prodrg charges
>>>>> (e.g
>>>>> http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ;
>>>>> http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ).
>>>>> Dr. Verli pointed out the use of semi-empirical methods such as RM1
>>>>> in cases not involving simulations with sulphate or phosphate
>>>>> groups
>>>>> (what i

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

2009-03-31 Thread Lucio Montero 
How can you test the "ligands" when you don't know if they REALLY bind to 
the protein?


--
From: "Ran Friedman, Biochemisches Inst." 
Sent: Friday, March 27, 2009 2:35 PM
To: ; "Discussion list for GROMACS users" 


Subject: Re: [gmx-users] HF/6-31G** ESP derived charges to replace  
PRODRGassignedones


Dear Josmar,

You haven't written which force field you plan to use. For OPLS and AMBER 
QM-based optimisation should be fine. In Gromos, the FF was developed with 
the aim of reproducing experimental results and I'm not sure if you can 
find a better solution than examining other residues with the same 
chemical moieties or use the same approach as reported in the relevant 
manuscripts. Some software packages can also be used - these are mostly 
proprietary and not so easy to use.


Once you derive the parameters, it's a good idea to make some test runs of 
the ligands and see if they behave as expected before you actually run a 
simulation with the protein. For example, if a conjugate ring system isn't 
planar something may be wrong in the setting.


There's no easy solution - this is why it's considered an advanced topic. 
It is, however, very important. I've encountered a ligand that leaves its 
binding site during a simulation due to wrong parameters (in this case, 
the protonation of a protein side chain - FEBS  581, Pages 4120-4124, 
2007).


Hope that helped,
Ran

On Fri, 27 Mar 2009 12:22:01 -0700 (PDT)
 "Josmar R. da Rocha"  wrote:

Dear users,

I have been reading some posts about using externally computed charges to 
replace Prodrg charges at ligand topology files. Many users commented on 
the low trustability given to Prodrg charges (e.g 
http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; 
http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ). Dr. 
Verli pointed out the use of semi-empirical methods such as RM1 in cases 
not involving simulations with sulphate or phosphate groups (what is not 
my case) and the use of QM methods with the 6-31G** basis set, for 
example, to obtain robust charges 
(http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On the 
other hand Dr. Mobley defined as a "a bad idea to compute charges for an 
all-atom case using QM and then try to convert these to a united atom 
force field". Other users advice that the best charges are that 
compatible with the force field parametrization
(http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ; 
http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html), usually 
pointing to http://wiki.gromacs.org/index.php/Parameterization. Dr 
Friedman suggested that "to calculate the electrostatic potential over 
the whole molecule, and fit the atomic charges so that they reproduce 
this potential" in order to make it less sensitive to small changes in 
the geometry of the molecule may give good results 
(http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html). Dr. 
Lemkul stressed the need for charges refinement to reproduce 
experimentally-observed behavior while trying to use QM charges with 
Gromos ff. since "Parameterization under Gromos usually involves 
empirical derivation of physical parameters, and free energy calculations 
using thermodynamic integration". Few examples of protein-ligand studies 
using Gromacs and Gromos96 ff that I have access (from literature) seem 
to treat it as "take it for granted" issue (any reference with a more 
detailed description would be welcome :-)). Despite reading on this topic 
I could not compile all the information in a clear and objective way (may 
be because I'm in the wrong track). Let ask you some question that I find 
would help me to make my ideas more clear:



1-am I overestimating the importance of ligand charges in such a simple 
study of protein-small molecule (containg charged Phosphate groups) 
complex? or


1.1-The only way to test for this is doing many different simulation on 
the same system using different type of computed charges to see what 
happen?


2-How could I try to choose a method to obtain reasonable charges based 
on the reproduction of experimentally-observed behavior if I do not have 
experimental data for my system?


3-I also would like to know from users dealing with protein-ligand 
interactions studies what do you consider a good approach to address this 
problem?


Based on what I read I'd have a tendency to use HF/6-31G** ESP derived 
charges (with necessary changes as to make it united-atom charges and 
scaling that to a integer number for each group). Please, let me know if 
that strategy would be as good as a disaster! Thank you very much for the 
attention.



Josmar Rocha



 Veja quais são os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com




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Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

2009-03-31 Thread Lucio Montero 
How about MOPAC to calculate the charges for 3-methyladenine (this molecule 
has a charge +1) for using the G43a1 force field?.



--
From: "Ran Friedman, Biochemisches Inst." 
Sent: Friday, March 27, 2009 2:35 PM
To: ; "Discussion list for GROMACS users" 


Subject: Re: [gmx-users] HF/6-31G** ESP derived charges to replace  
PRODRGassignedones


Dear Josmar,

You haven't written which force field you plan to use. For OPLS and AMBER 
QM-based optimisation should be fine. In Gromos, the FF was developed with 
the aim of reproducing experimental results and I'm not sure if you can 
find a better solution than examining other residues with the same 
chemical moieties or use the same approach as reported in the relevant 
manuscripts. Some software packages can also be used - these are mostly 
proprietary and not so easy to use.


Once you derive the parameters, it's a good idea to make some test runs of 
the ligands and see if they behave as expected before you actually run a 
simulation with the protein. For example, if a conjugate ring system isn't 
planar something may be wrong in the setting.


There's no easy solution - this is why it's considered an advanced topic. 
It is, however, very important. I've encountered a ligand that leaves its 
binding site during a simulation due to wrong parameters (in this case, 
the protonation of a protein side chain - FEBS  581, Pages 4120-4124, 
2007).


Hope that helped,
Ran

On Fri, 27 Mar 2009 12:22:01 -0700 (PDT)
 "Josmar R. da Rocha"  wrote:

Dear users,

I have been reading some posts about using externally computed charges to 
replace Prodrg charges at ligand topology files. Many users commented on 
the low trustability given to Prodrg charges (e.g 
http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; 
http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ). Dr. 
Verli pointed out the use of semi-empirical methods such as RM1 in cases 
not involving simulations with sulphate or phosphate groups (what is not 
my case) and the use of QM methods with the 6-31G** basis set, for 
example, to obtain robust charges 
(http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On the 
other hand Dr. Mobley defined as a "a bad idea to compute charges for an 
all-atom case using QM and then try to convert these to a united atom 
force field". Other users advice that the best charges are that 
compatible with the force field parametrization
(http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ; 
http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html), usually 
pointing to http://wiki.gromacs.org/index.php/Parameterization. Dr 
Friedman suggested that "to calculate the electrostatic potential over 
the whole molecule, and fit the atomic charges so that they reproduce 
this potential" in order to make it less sensitive to small changes in 
the geometry of the molecule may give good results 
(http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html). Dr. 
Lemkul stressed the need for charges refinement to reproduce 
experimentally-observed behavior while trying to use QM charges with 
Gromos ff. since "Parameterization under Gromos usually involves 
empirical derivation of physical parameters, and free energy calculations 
using thermodynamic integration". Few examples of protein-ligand studies 
using Gromacs and Gromos96 ff that I have access (from literature) seem 
to treat it as "take it for granted" issue (any reference with a more 
detailed description would be welcome :-)). Despite reading on this topic 
I could not compile all the information in a clear and objective way (may 
be because I'm in the wrong track). Let ask you some question that I find 
would help me to make my ideas more clear:



1-am I overestimating the importance of ligand charges in such a simple 
study of protein-small molecule (containg charged Phosphate groups) 
complex? or


1.1-The only way to test for this is doing many different simulation on 
the same system using different type of computed charges to see what 
happen?


2-How could I try to choose a method to obtain reasonable charges based 
on the reproduction of experimentally-observed behavior if I do not have 
experimental data for my system?


3-I also would like to know from users dealing with protein-ligand 
interactions studies what do you consider a good approach to address this 
problem?


Based on what I read I'd have a tendency to use HF/6-31G** ESP derived 
charges (with necessary changes as to make it united-atom charges and 
scaling that to a integer number for each group). Please, let me know if 
that strategy would be as good as a disaster! Thank you very much for the 
attention.



Josmar Rocha



 Veja quais são os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com




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

2009-03-13 Thread Lucio Montero 
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.
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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Re: [gmx-users] simulation box

2009-03-04 Thread Lucio Montero 
If you use periodic boundaries, the box size needs to be more than twice the 
cutoffs, to avoid calculation errors. I found this advice in the manual. (I 
though reading it was a time waste, but more time I was going to waste doing 
a wrong 1 ns simulation on a big system).


--
From: "Justin A. Lemkul" 
Sent: Tuesday, March 03, 2009 12:00 PM
To: ; "Discussion list for GROMACS users" 


Subject: Re: [gmx-users] simulation box


Quoting Ricardo Soares :


noob noob wrote:
>
> Dear all,
>
>  I am new about MD simulation and I have some questions about the box
> size.
>
> I had performed 1 simulation previously ( box size of 5 nm x 5 nm x 5
> nm ) but now I change to a bigger molecules and increase the number of
> molecules. So,the new system cannot fix into the previous box.
> Therefore, I tried to Increase my box to a bigger one ( 20 nm x 20 nm
> x 20 nm) which can fix the system nicely.
>
> So, is it compulsory to use certain box size in our system? or we just 
> use

> any box size which our molecules can fix into it, then perform MD?
>
Sorry, I didn't see this other question of yours.
If you use a box that is much larger than the main molecule, you will
need lots of water, which will be time-consuming. Otherwise, if you use
a very small box, it may compromise the free movement of the protein.
So i say the best option is to scale the box size according to your
specific molecule size. This is done within the editconf program. (see
the gromacs manual for further reference).



In addition, you need to consider cutoff lengths and periodic boundary
conditions/minimum image convention.  Some textbook reading is in order.

-Justin


Cheers,

Ricardo.


> Sorry for the "stupid" questions.
>
> thanks for the comments.
>
>
> Alvin Chan.
> 
> check out the rest of the Windows LiveT. More than mail-Windows LiveT
> goes way beyond your inbox. More than messages
> 
> 
>
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Ricardo Oliveira dos Santos Soares
Post-graduation Student in Biological Physics
University of Sao Paulo - USP
Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
Phone: 55 (16) 3602-4840
Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
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Justin A. Lemkul
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalem...@vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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

2009-02-25 Thread Lucio Montero 

Thanks very much.
 Lucio Montero.

--
From: "Justin A. Lemkul" 
Sent: Wednesday, February 25, 2009 5:55 AM
To: "Discusson list for GROMACS users" 
Subject: Re: [gmx-users] OPLS-AA topologies for ATP/ADP.




Lucio Ricardo Montero Valenzuela 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?.


Methods for parameterization can be found in the primary literature for 
the force field.  A few notes on this advanced topic:


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

-Justin


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


Este mensaje fue enviado desde el servidor Webmail del Instituto de 
Biotecnologia.

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Justin A. Lemkul
Graduate Research Assistant
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] How to show the created box?

2009-02-16 Thread Lucio Montero 
If your box is very big, VMD may run out all your computer's memory and 
crash. You can copy your GRO file and erase some water molecules in the 
middle of the GRO file copy, for you see the extremes of your water box.

Kind regards.

--
From: "Mark Abraham" 
Sent: Sunday, February 15, 2009 10:33 PM
To: "Discussion list for GROMACS users" 
Subject: Re: [gmx-users] How to show the created box?


Chih-Ying Lin wrote:

HI
after creating the box, and write it into .gro file.

when i try the .gro file with VMD, but the box is not shown.

how can i show the created box with VMD?


You should start by looking in the VMD help and/or manual :-)

Mark
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[gmx-users] Force field selection

2008-12-04 Thread Lucio Montero 
Hello!
What is the best force field to use for a MD of a compley of three proteins and 
an organic molecule. And what are the best temperature and pressure coupling 
methods.
Best regards.
  Lucio.___
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Re: [gmx-users] Integration of a carbonate ion to GROMACS V3.3

2008-09-29 Thread Lucio Montero 
If you are using the GROMOS96, the forcefield files are ffG.*. ffgmx are 
for the GROMACS forcefield (that is deprecated). The forcefield file titles 
are listed in the file FF.dat in the gromacs topology directory. Here are 
the contents of my FF.dat file:

11
ffG43a1  GROMOS96 43a1 force field
ffG43b1  GROMOS96 43b1 vacuum force field
ffG43a2  GROMOS96 43a2 force field (improved alkane dihedrals)
ffG45a3  GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
ffG53a5  GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
ffG53a6  GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
ffoplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
ffgmx[DEPRECATED] Gromacs force field (see manual)
ffgmx2   [DEPRECATED] Gromacs force field with hydrogens for NMR
ffencadv Encad all-atom force field, using scaled-down vacuum charges
ffencads Encad all-atom force field, using full solvent charges
---
Hope this helps.

--
From: "Fabian Homberg" <[EMAIL PROTECTED]>
Sent: Saturday, September 27, 2008 7:09 AM
To: 
Subject: [gmx-users] Integration of a carbonate ion to GROMACS V3.3


Dear GROMACS-team,

i have a problem with the integration of a carbonate ion (CO3 ^2-) to
GROMACS, because i want to simulate a mixture of tip4p-water with
solvated potassium carbonate and the carbonate ion is not integrated
in the standard version.
After having read  „balamurugan r biobee at rediffmail.com"'s problem,
which is almost the same i have, i tried to integrate:

[CO3]
 [atoms]
OAA OM  -0.221  0
CAC  C  0.494  1
OAB  OM  -0.221 0
OAD  OM  -0.052 2

to the ffgmx.rtp-file (I am using the GROMOS-96 standard force field: 
ffgmx.*).

Then i went on with adding:

[ moleculetype ]
; molname   nrexcl
CO3-1

[ atoms ]
; idat type res nr  residu name at name  cg nr  charge   mass
1   CO3-1   CO3-CO3- 1  -2   60.00800

to the ions.itp-file.
Finally i tried to get the system ready for an energy-minimization
with the command
"grompp -f em -p topol -o topol -c conf -n index",
but then a fatal error occurred:
"No such moleculetype CO3"

So i went on trying to integrate:

[ moleculetype ]
; Name nrexcl
CO3  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
   1OM 1  CO3 OAA 1   -0.221  15.9994
   2 C 1  CO3 CAC 10.494  12.0110
   3OM 1  CO3 OAB 1   -0.221  15.9994
   4OM 1  CO3 OAD 1   -0.052  15.9994

[ bonds ]
; ai  aj  fuc0, c1, ...
 1   2   10.125418400.00.125418400.0 ;   OAA  CAC
 2   3   10.125418400.00.125418400.0 ;   CAC  OAB
 2   4   10.125418400.00.125418400.0 ;   CAC  OAD

[ pairs ]
; ai  aj  fuc0, c1, ...

[ angles ]
; ai  aj  ak  fuc0, c1, ...
 1   2   3   1126.0   502.1126.0   502.1 ;   OAA  CAC  OAB
 1   2   4   1126.0   502.1126.0   502.1 ;   OAA  CAC  OAD
 3   2   4   1126.0   502.1126.0   502.1 ;   OAB  CAC  OAD

[ dihedrals ]
; ai  aj  ak  al  fuc0, c1, m, ...
 2   4   3   1   2  0.0 1673.6 0  0.0 1673.6 0 ; imp   CAC
OAD  OAB  OAA
to the .itp-file, but it still doesn't work.

Do you have advice to solve this problem?


Best regards

Fabian Homberg
Student assistant at
Lehrstuhl für Thermodynamik (LTD)
TU Kaiserslautern, Germany
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Re: [gmx-users] Re:Question regarding Gromacs

2008-09-29 Thread Lucio Montero 
If you are doing simulated annealing, your system explode if you are heating 
all the system (protein and water). Divide your system in protein and water 
and heat only the protein.


--
From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]>
Sent: Monday, September 29, 2008 2:50 AM
To: "minnale" <[EMAIL PROTECTED]>; "Discussion list for GROMACS 
users" 

Subject: Re: [gmx-users] Re:Question regarding Gromacs


Minnale,


Thanks for the reply, what may be the reason GROMACS became great?


Check the JCC 2005 paper: http://www.ncbi.nlm.nih.gov/pubmed/16211538


  sometimes though system explodes it will generate energy minimisation
output.gro file we cant use this file for further run?


Need more information..., what did you try to do? Did you do EM? Check
for overlaps, go through your system carefully, don't stick your head
in the sand and continue the simulation. Mind you that MD programs
adhere to the Rubbish-in Rubbish-out protocol (RRP :p).

Cheers,

Tsjerk

--
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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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