Re: [gmx-users] please, how edr data is xdr packed?

2010-08-23 Thread Sander Pronk 
As David said, the reading/writing is done in src/gmxlib/enxio.c, but you could 
also read edr files indirectly through gmxdump: that should also give you an 
idea of the type of information in those files.



On Aug 22, 2010, at 13:14 , Alan Wilter Sousa da Silva wrote:

> Hi there,
> 
> I am trying to use python xdrlib module to read edr files but not knowing how 
> the data is packed using the xdr protocol makes my work very difficult, if 
> not impossible.
> 
> Would someone kindly tell me how data is packed in the edr file? Or where it 
> is the gromacs code so I can try to figure out a way?
> 
> I've read http://tools.ietf.org/html/rfc1832.html and for reference, see 
> topic "6. AN EXAMPLE OF AN XDR DATA DESCRIPTION".
> 
> My other option would be using a parsing code to read g_energy output but 
> this seems very silly.
> 
> Many thanks in advance,
> 
> Alan
> 
> -- 
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge. 
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
> -- 
> gmx-users mailing listgmx-users@gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] PMF

2010-08-23 Thread Justin A. Lemkul 



abdul wadood wrote:

Hi, All

I am trying to calculate pmf for enzyme ligand complex using the 
tutorial of umbrella sampling.
I have successfully created the unit cell around the protein and have 
solvated. The ions were also added by genion.

But when I run the minimization step with the command

grompp -f minim.mdp -c solv_ions.gro -p 3JY0.top -o em.tpr


the following error comes


Fatal error:
Molecule type 'NA+' contains no atoms


I tried my best to solve the problem but could no succeeded.


This is a useless statement.  What exactly have you tried?  You will receive 
help much more efficiently if we know exactly what has worked and what hasn't. 
It sounds like a simple problem - you've defined NA+ ions in the topology, but 
there aren't any in your system.  Be sure that you're not following the tutorial 
too literally.  That is, just because the tutorial said to add NA+ to that 
particular system doesn't mean you'll necessarily have NA+ in every system.


-Justin


Any help to solve this problem will be highly appreciated.
The topology file is attached.

Thanks in advace

Many regards

Abdul Wadood,
Research Scholar,
Dr.Panjwani Center for Molecular Medicine and
Drug Research,
International Center for Chemical and
Biological Science,
University of Karachi, Karachi-75720, Pakistan.
Email:wadoodbiochem...@hotmail.com




--


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


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Re: [gmx-users] Charmm to Gromacs: Polyols force field [Justin]

2010-08-23 Thread Justin A. Lemkul 
 > ___
 > Eudes Eterno Fileti
 > Centro de Ciências Naturais e Humanas
 > Universidade Federal do ABC — CCNH
 > Av. dos Estados, 5001
 > Santo André - SP - Brasil
 > CEP 09210-971
 > +55.11.4996-0196
 > http://fileti.ufabc.edu.br
 >

--


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




--

Message: 4
Date: Mon, 23 Aug 2010 06:23:39 +
From: abdul wadood mailto:wadoodbiochem...@hotmail.com>>
Subject: [gmx-users] PMF
To: gromacs mailto:gmx-users@gromacs.org>>
Message-ID: 
Content-Type: text/plain; charset="iso-8859-1"


Hi, All

I am trying to calculate pmf for enzyme ligand complex using the
tutorial of umbrella sampling.
I have successfully created the unit cell around the protein and
have solvated. The ions were also added by genion.
But when I run the minimization step with the command
grompp -f minim.mdp -c solv_ions.gro -p 3JY0.top -o em.tpr
the following error comes


Fatal error:
Molecule type 'NA+' contains no atoms


I tried my best to solve the problem but could no succeeded.
Any help to solve this problem will be highly appreciated.
The topology file is attached.

Thanks in advace

Many regards

Abdul Wadood,
Research Scholar,
Dr.Panjwani Center for Molecular Medicine and
Drug Research,
International Center for Chemical and
Biological Science,
University of Karachi, Karachi-75720, Pakistan.
Email:wadoodbiochem...@hotmail.com
<mailto:email%3awadoodbiochem...@hotmail.com>



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Message: 5
Date: Mon, 23 Aug 2010 09:56:26 +0200
From: Sander Pronk mailto:pr...@cbr.su.se>>
Subject: Re: [gmx-users] please, how edr data is xdr packed?
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID: <31d44996-834b-4f78-8880-81320fe9e...@cbr.su.se
<mailto:31d44996-834b-4f78-8880-81320fe9e...@cbr.su.se>>
Content-Type: text/plain; charset="us-ascii"

As David said, the reading/writing is done in src/gmxlib/enxio.c,
but you could also read edr files indirectly through gmxdump: that
should also give you an idea of the type of information in those files.



On Aug 22, 2010, at 13:14 , Alan Wilter Sousa da Silva wrote:

 > Hi there,
 >
 > I am trying to use python xdrlib module to read edr files but not
knowing how the data is packed using the xdr protocol makes my work
very difficult, if not impossible.
 >
 > Would someone kindly tell me how data is packed in the edr file?
Or where it is the gromacs code so I can try to figure out a way?
 >
 > I've read http://tools.ietf.org/html/rfc1832.html and for
reference, see topic "6. AN EXAMPLE OF AN XDR DATA DESCRIPTION".
 >
 > My other option would be using a parsing code to read g_energy
output but this seems very silly.
 >
 > Many thanks in advance,
 >
 > Alan
 >
 > --
 > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
 > Department of Biochemistry, University of Cambridge.
 > 80 Tennis Court Road, Cambridge CB2 1GA, UK.
 > >>http://www.bio.cam.ac.uk/~awd28<<
 > --
 > gmx-users mailing listgmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
     > Please search the archive at http://www.gromacs.org/search before
posting!
 > Please don't post (un)subscribe requests to the list. Use the
 > www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
 > Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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p

[gmx-users] g_hbond

2010-08-23 Thread pawan raghav 
 Below is the hbond.xvg content 1 coloumn is for time second for numbers,
but I am not getting for 3rd one i.e. Pairs within 0.35 nm is this shows
area in cutoff range?

@ title "Hydrogen Bonds"

@ xaxis label "Time"

@ yaxis label "Number"

@TYPE xy

@ view 0.15, 0.15, 0.75, 0.85

@ legend on

@ legend box on

@ legend loctype view

@ legend 0.78, 0.8

@ legend length 2

@ s0 legend "Hydrogen bonds"

@ s1 legend "Pairs within 0.35 nm"

0 2 175

3 2 188

6 3 190

9 4 190

12 2 190

15 3 182

18 0 183

21 3 179


-- 
Pawan
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Re: [gmx-users] Charmm to Gromacs: Polyols force field [Justin]

2010-08-23 Thread Eudes Fileti 
t; From: abdul wadood 
> Subject: [gmx-users] PMF
> To: gromacs 
> Message-ID: 
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hi, All
>
> I am trying to calculate pmf for enzyme ligand complex using the tutorial
> of umbrella sampling.
> I have successfully created the unit cell around the protein and have
> solvated. The ions were also added by genion.
> But when I run the minimization step with the command
> grompp -f minim.mdp -c solv_ions.gro -p 3JY0.top -o em.tpr
> the following error comes
>
>
> Fatal error:
> Molecule type 'NA+' contains no atoms
>
>
> I tried my best to solve the problem but could no succeeded.
> Any help to solve this problem will be highly appreciated.
> The topology file is attached.
>
> Thanks in advace
>
> Many regards
>
> Abdul Wadood,
> Research Scholar,
> Dr.Panjwani Center for Molecular Medicine and
> Drug Research,
> International Center for Chemical and
> Biological Science,
> University of Karachi, Karachi-75720, Pakistan.
> Email:wadoodbiochem...@hotmail.com 
>
>
>
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> http://lists.gromacs.org/pipermail/gmx-users/attachments/20100823/6c9f9ed2/attachment-0001.html
>
> --
>
> Message: 5
> Date: Mon, 23 Aug 2010 09:56:26 +0200
> From: Sander Pronk 
> Subject: Re: [gmx-users] please, how edr data is xdr packed?
> To: Discussion list for GROMACS users 
> Message-ID: <31d44996-834b-4f78-8880-81320fe9e...@cbr.su.se>
> Content-Type: text/plain; charset="us-ascii"
>
> As David said, the reading/writing is done in src/gmxlib/enxio.c, but you
> could also read edr files indirectly through gmxdump: that should also give
> you an idea of the type of information in those files.
>
>
>
> On Aug 22, 2010, at 13:14 , Alan Wilter Sousa da Silva wrote:
>
> > Hi there,
> >
> > I am trying to use python xdrlib module to read edr files but not knowing
> how the data is packed using the xdr protocol makes my work very difficult,
> if not impossible.
> >
> > Would someone kindly tell me how data is packed in the edr file? Or where
> it is the gromacs code so I can try to figure out a way?
> >
> > I've read http://tools.ietf.org/html/rfc1832.html and for reference, see
> topic "6. AN EXAMPLE OF AN XDR DATA DESCRIPTION".
> >
> > My other option would be using a parsing code to read g_energy output but
> this seems very silly.
> >
> > Many thanks in advance,
> >
> > Alan
> >
> > --
> > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> > Department of Biochemistry, University of Cambridge.
> > 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> > >>http://www.bio.cam.ac.uk/~awd28<<
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
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Re: [gmx-users] g_hbond

2010-08-23 Thread Justin A. Lemkul 



pawan raghav wrote:
Below is the hbond.xvg content 1 coloumn is for time second for numbers, 
but I am not getting for 3rd one i.e. Pairs within 0.35 nm is this shows 
area in cutoff range?
 


Search the mailing list archive.  I answered this identical question last week. 
   If you use the phrase "g_hbond third column" (without quotes) you'll find 
your answer.


-Justin


@ title "Hydrogen Bonds"

@ xaxis label "Time"

@ yaxis label "Number"

@TYPE xy

@ view 0.15, 0.15, 0.75, 0.85

@ legend on

@ legend box on

@ legend loctype view

@ legend 0.78, 0.8

@ legend length 2

@ s0 legend "Hydrogen bonds"

@ s1 legend "Pairs within 0.35 nm"

0 2 175

3 2 188

6 3 190

9 4 190

12 2 190

15 3 182

18 0 183

21 3 179



--
Pawan



--


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


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[gmx-users] Attempting to scale gromacs mdrun_mpi

2010-08-23 Thread NG HUI WEN 
Hi,
 
I have been playing with the "mdrun_mpi" command in gromacs 4.0.7 to try out  
parallel processing. Unfortunately, the results I got did not show any 
significant improvement in simulation time.
 
Below is the command I issued:
 
mpirun -np x mdrun_mpi  -deffnm
 
where x is the number of processors being used.
 
>From the machine output, it seemed that the work had indeed been distributed 
>to multiple processors e.g. -np 10:
NNODES=10, MYRANK=5, HOSTNAME=beowulf
NODEID=4 argc=3
NNODES=10, MYRANK=1, HOSTNAME=beowulf
NNODES=10, MYRANK=2, HOSTNAME=beowulf
NODEID=1 argc=3
NODEID=9 argc=3
NODEID=5 argc=3
NNODES=10, MYRANK=3, HOSTNAME=beowulf
NNODES=10, MYRANK=7, HOSTNAME=beowulf
NNODES=10, MYRANK=8, HOSTNAME=beowulf
NODEID=8 argc=3
NODEID=2 argc=3
NODEID=6 argc=3
NODEID=3 argc=3
NODEID=7 argc=3
Making 2D domain decomposition 5 x 1 x 2
starting mdrun 'PROTEIN'
1000 steps,  2.0 ps.
 
The simulation system consists of 100581 atoms, the duration is 2ps (1000 
steps). results obtained are as followed:
 
number of CPUs   Simulation time
1  13m28s
2 6m31s
3 7m33s
4  6m47s
5  7m48s
6  6m55s
7  7m36s
8  6m58s
9  7m15s
107m01s
157m27s
207m15s
307m42s
 
Significant improvement in simulation time was only observed from -np 1 to 2.  
As almost all (except -np = 1) complaint about load imbalance and PP:PME 
imbalance (the latter was  seen especially in those with larger -np value), I 
tried to increase the pme nodes by adding a -npme flag and entered a bigger 
number but the results either showed no improvement or worsened.
 
As I am new to gromacs, there might be some things that I'd missed out/done 
incorrectly. Would really appreciate some input to this. Many thanks in 
advance!!
 
HW
<< Email has been scanned for viruses by UNMC email management service >>
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Re: [gmx-users] Attempting to scale gromacs mdrun_mpi

2010-08-23 Thread Roland Schulz 
Hi,

you don't write what network you have and how many cores per node. If it is
ethernet it will be difficult to scale.
You might want to try the 4.5beta version because we have improved the
scaling with it. Also there is a tool g_tune_pme which might help you.

Roland

On Mon, Aug 23, 2010 at 11:15 AM, NG HUI WEN wrote:

>  Hi,
>
>
>
> I have been playing with the “mdrun_mpi” command in gromacs 4.0.7 to try
> out  parallel processing. Unfortunately, the results I got did not show
> any significant improvement in simulation time.
>
>
>
> Below is the command I issued:
>
>
>
> mpirun –np x mdrun_mpi  -deffnm
>
>
>
> where x is the number of processors being used.
>
>
>
> From the machine output, it seemed that the work had indeed been
> distributed to multiple processors e.g. -np 10:
>
> NNODES=10, MYRANK=5, HOSTNAME=beowulf
> NODEID=4 argc=3
> NNODES=10, MYRANK=1, HOSTNAME=beowulf
> NNODES=10, MYRANK=2, HOSTNAME=beowulf
> NODEID=1 argc=3
> NODEID=9 argc=3
> NODEID=5 argc=3
> NNODES=10, MYRANK=3, HOSTNAME=beowulf
> NNODES=10, MYRANK=7, HOSTNAME=beowulf
> NNODES=10, MYRANK=8, HOSTNAME=beowulf
> NODEID=8 argc=3
> NODEID=2 argc=3
> NODEID=6 argc=3
> NODEID=3 argc=3
> NODEID=7 argc=3
> Making 2D domain decomposition 5 x 1 x 2
> starting mdrun 'PROTEIN'
> 1000 steps,  2.0 ps.
>
>
>
> The simulation system consists of 100581 atoms, the duration is 2ps (1000
> steps). results obtained are as followed:
>
>
>
> *number of CPUs   Simulation time*
>
> 1  13m28s
>
> 2 6m31s
>
> 3 7m33s
>
> 4  6m47s
>
> 5  7m48s
>
> 6  6m55s
>
> 7  7m36s
>
> 8  6m58s
>
> 9  7m15s
>
> 107m01s
>
> 157m27s
>
> 207m15s
>
> 307m42s
>
>
>
> Significant improvement in simulation time was only observed from -np 1 to
> 2.  As almost all (except -np = 1) complaint about load imbalance and PP:PME
> imbalance (the latter was  seen especially in those with larger -np value),
> I tried to increase the pme nodes by adding a -npme flag and entered a
> bigger number but the results either showed no improvement or worsened.
>
>
>
> As I am new to gromacs, there might be some things that I'd missed out/done
> incorrectly. Would really appreciate some input to this. Many thanks in
> advance!!
>
>
>
> HW
> <<
>
> Email has been scanned for viruses by UNMC email management 
> service
> >>
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>



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865-241-1537, ORNL PO BOX 2008 MS6309
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Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Justin]

2010-08-23 Thread Eudes Fileti 
Hello Justin, thanks again.
Well, the line 40 is just one of the 36 parameters not found!
In this link ( https://sites.google.com/site/fileti/ ) I put the complete
files.
I know I need to determine which bond type should be called and I believe
that it has been done, but I don't know why it's not being found.

The order of atoms in the link could be the cause of error?
Ie, CA-CB would be different from CB-CA, or HO-OH-CB would be different from
CB-OH-HO?

If possible you take a quick conferred and gave me some guidance, it would
be great!
Bests



Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC - CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4996-0196
http://fileti.ufabc.edu.br
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Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Justin]

2010-08-23 Thread Mark Abraham 


- Original Message -
From: Eudes Fileti 
Date: Tuesday, August 24, 2010 2:12
Subject: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Justin]
To: gmx-users@gromacs.org

> Hello Justin, thanks again.> Well, the line 40 is just one of the 36 
> parameters not found!> In this link ( https://sites.google.com/site/fileti/ ) 
> I put the complete files.  > I know I need to determine which bond type 
> should be called and I believe > that it has been done, but I don't know why 
> it's not being found.

You've got heaps more problems than that. The file you say is ffbonded.itp is 
different from the one grompp is finding, because yours doesn't have 1492 lines 
in it, and grompp says there's an error there.

I suspect you've started editing in your installation share/gromacs/top folder 
and gotten things confused. It will be best to start afresh with a fresh 
installation (and thus copy of share/gromacs/top). Or CHARMM in beta3 is badly 
broken somehow...

> The order of atoms in the link could be the cause of error?  > Ie, CA-CB 
> would be different from CB-CA, or HO-OH-CB would be different from CB-OH-HO?

No, grompp deals with atom order sensibly.

Mark
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[gmx-users] issue with pdb2gmx 4.5 and HISE oplsaa

2010-08-23 Thread Alan 
Hi there,

I have a system with 'HISE' and using gmx 4.5.

ATOM 20  N   HISE2   6.376   3.718  -0.053  1.00  0.00
N
ATOM 21  H   HISE2   5.980   4.646  -0.135  1.00  0.00
H
ATOM 22  CA  HISE2   7.843   3.744  -0.109  1.00  0.00
C
ATOM 23  HA  HISE2   8.260   3.319   0.806  1.00  0.00
H
ATOM 24  CB  HISE2   8.319   2.925  -1.327  1.00  0.00
C
ATOM 25  HB2 HISE2   7.855   1.940  -1.312  1.00  0.00
H
ATOM 26  HB1 HISE2   7.985   3.435  -2.233  1.00  0.00
H
ATOM 27  CG  HISE2   9.807   2.703  -1.450  1.00  0.00
C
ATOM 28  ND1 HISE2  10.461   2.463  -2.655  1.00  0.00
N
ATOM 29  CE1 HISE2  11.770   2.542  -2.382  1.00  0.00
C
ATOM 30  HE1 HISE2  12.557   2.484  -3.124  1.00  0.00
H
ATOM 31  NE2 HISE2  11.969   2.794  -1.078  1.00  0.00
N
ATOM 32  HE2 HISE2  12.817   3.173  -0.672  1.00  0.00
H
ATOM 33  CD2 HISE2  10.740   2.839  -0.459  1.00  0.00
C
ATOM 34  HD2 HISE2  10.579   3.098   0.574  1.00  0.00
H
ATOM 35  C   HISE2   8.279   5.228  -0.214  1.00  0.00
C
ATOM 36  O   HISE2   7.440   6.079  -0.525  1.00  0.00
O

when trying:

pdb2gmx -f oHHH.pdb -o ogHHH.pdb -p ogHHH.top -ff oplsaa -water none

Identified residue HISE1 as a starting terminus.
Identified residue HISE3 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
   HISE1   HISE2
   NE214   NE231
   HISE2   NE231   0.854
   HISE3   NE248   0.751   0.847
Start terminus: NH3+
End terminus: COO-

---
Program pdb2gmx, VERSION 4.5-beta3-dev-20100812-97d39
Source code file: /Users/alan/Programmes/gromacs/src/kernel/pdb2gmx.c, line:
583

Fatal error:
Atom HE2 in residue HISE 1 not found in rtp entry HIS1 with 19 atoms
while sorting atoms. Maybe different protonation state.
 Remove this hydrogen or choose a different protonation state.
 Option -ignh will ignore all hydrogens in the input.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Why error is referencing to HIS1 (= HISA = HISD in OPLS terminology, hence
!= HISE)

Many thanks in advance,

Alan
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Re: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Mark]

2010-08-23 Thread Eudes Fileti 
Hello Mark thanks for the comments,
In fact, what I did was insert the parameters into ffbonded.itp file.
What I presented the link above is just the part that I had added
(of course there is the line 1495, not shown!).

The installation where I started making the change is new,
I have not changed anything, just added the lines for the parameters
mentioned.
Nevertheless, you think I need to re-install the gromacs?

Bests
eef
___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4996-0196
http://fileti.ufabc.edu.br
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[gmx-users] g_dist issue

2010-08-23 Thread teklebrh 

Dear Gromacs users,

I run my simulation for 20ns and want to extract aromatic-aromatic  
distance to see the stacking issue. But I am unable to get the value.


I have 24 molecules in my simulation and filled with solvents.

My index file is like that:

[ System ]
   123456789   10   11   12   13   14   15
  16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
  31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
  46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
  61   62
  '''
  '''
  '''
  ''

[ RING ]
  19   20   21   22   23   24   25   26   27   28   29   30
  32   34   37   38   39   40   42   44

This is the ring I created plane in the index file.

I used this command line

g_dist -f PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2 -o  
DistPAP8HEP.xvg


but got the following like

I want to get the mean separation distance between two consecutive  
polyaromatic rings along the axis of stacking


can someone help.

rob



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Re: [gmx-users] g_dist issue( Out put file)

2010-08-23 Thread teklebrh 

The following is the out put.

# This file was created Mon Aug 23 11:18:45 2010
# by the following command:
# /home/software/gromacs/3.3.3/bin/g_dist -f  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2 -o  
DistPAP8HEP.xvg

#
# /home/software/gromacs/3.3.3/bin/g_dist is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.0000.0000.0000.000
19002.0000.0000.0000.0000.000
19004.0000.0000.0000.0000.000
19006.0000.0000.0000.0000.000
19008.0000.0000.0000.0000.000
19010.0000.0000.0000.0000.000
19012.0000.0000.0000.0000.000
19014.0000.0000.0000.0000.000
19016.0000.0000.0000.0000.000
19018.0000.0000.0000.0000.000
19020.0000.0000.0000.0000.000
19022.0000.0000.0000.0000.000
19024.0000.0000.0000.0000.000
19026.0000.0000.0000.0000.000
19028.0000.0000.0000.0000.000
19030.0000.0000.0000.0000.000
19032.0000.0000.0



Quoting tekle...@ualberta.ca:


Dear Gromacs users,

I run my simulation for 20ns and want to extract aromatic-aromatic  
distance to see the stacking issue. But I am unable to get the value.


I have 24 molecules in my simulation and filled with solvents.

My index file is like that:

[ System ]
   123456789   10   11   12   13   14   15
  16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
  31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
  46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
  61   62
  '''
  '''
  '''
  ''

[ RING ]
  19   20   21   22   23   24   25   26   27   28   29   30
  32   34   37   38   39   40   42   44

This is the ring I created plane in the index file.

I used this command line

g_dist -f PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2  
-o DistPAP8HEP.xvg


but got the following like

I want to get the mean separation distance between two consecutive  
polyaromatic rings along the axis of stacking


can someone help.

rob



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Re: [gmx-users] g_dist issue( Out put file)

2010-08-23 Thread Justin A. Lemkul 



tekle...@ualberta.ca wrote:

The following is the out put.

# This file was created Mon Aug 23 11:18:45 2010
# by the following command:
# /home/software/gromacs/3.3.3/bin/g_dist -f 
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s 
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2 -o 
DistPAP8HEP.xvg

#
# /home/software/gromacs/3.3.3/bin/g_dist is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.0000.0000.0000.000
19002.0000.0000.0000.0000.000
19004.0000.0000.0000.0000.000
19006.0000.0000.0000.0000.000
19008.0000.0000.0000.0000.000
19010.0000.0000.0000.0000.000
19012.0000.0000.0000.0000.000
19014.0000.0000.0000.0000.000
19016.0000.0000.0000.0000.000
19018.0000.0000.0000.0000.000
19020.0000.0000.0000.0000.000
19022.0000.0000.0000.0000.000
19024.0000.0000.0000.0000.000
19026.0000.0000.0000.0000.000
19028.0000.0000.0000.0000.000
19030.0000.0000.0000.0000.000
19032.0000.0000.0



You say you want the distance between two rings, but you only showed an index 
group for one of them (presumably), and the fact that you've gotten all zeroes 
as a result would suggest that you chose the same group twice for the distance 
calculation.  Which groups did you select?  Do they correspond to two, 
non-overlapping index groups?


-Justin




Quoting tekle...@ualberta.ca:


Dear Gromacs users,

I run my simulation for 20ns and want to extract aromatic-aromatic 
distance to see the stacking issue. But I am unable to get the value.


I have 24 molecules in my simulation and filled with solvents.

My index file is like that:

[ System ]
   123456789   10   11   12   13   
14   15
  16   17   18   19   20   21   22   23   24   25   26   27   28   
29   30
  31   32   33   34   35   36   37   38   39   40   41   42   43   
44   45
  46   47   48   49   50   51   52   53   54   55   56   57   58   
59   60

  61   62
  '''
  '''
  '''
  ''

[ RING ]
  19   20   21   22   23   24   25   26   27   28   29   30
  32   34   37   38   39   40   42   44

This is the ring I created plane in the index file.

I used this command line

g_dist -f PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s 
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2 -o 
DistPAP8HEP.xvg


but got the following like

I want to get the mean separation distance between two consecutive 
polyaromatic rings along the axis of stacking


can someone help.

rob



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--


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


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Re: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Mark]

2010-08-23 Thread Mark Abraham 


- Original Message -
From: Eudes Fileti 
Date: Tuesday, August 24, 2010 3:22
Subject: Re: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Mark]
To: gmx-users@gromacs.org

> Hello Mark thanks for the comments,
> In fact, what I did was insert the parameters into ffbonded.itp file. 
> What I presented the link above is just the part that I had added 
> (of course there is the line 1495, not shown!).
 > 
> The installation where I started making the change is new, 
> I have not changed anything, just added the lines for the parameters 
> mentioned. 
> Nevertheless, you think I need to re-install the gromacs?

You shouldn't be editing ffbonded.itp directly, because now you've got no way 
short of a re-installation to go back at start afresh. Instead, copy the whole 
of charmm27.ff directory to your working directory, and edit *that*. So maybe, 
you do need to re-install, but perhaps save a copy of what you've already done 
so far - much of it is probably worthwhile :-)

As Justin's told you, you need to go and look at the lines that grompp is 
telling you are wrong. You've now shown us inserted bits twice - but those are 
useless to us because we don't have the context to know which is line 1492. If 
we were blessed with infinite time and patience, we might spot your problem 
without the context. However you already have a tool for spotting problems - 
grompp! So we're not inclined to spend much effort when you can at least 
identify the offending line for us in about 5 seconds with vi :-) Once you've 
found the line, check you've formatted it correctly.

Mark

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[gmx-users] GB Parameters

2010-08-23 Thread Elizabeth Ploetz 
Dear Gromacs Users, 

I am interested in implementing implicit solvent using the OBC GBSA method.  In 
the Gromacs 4.5beta3 top directory, several force fields (oplsaa and multiple 
versions of amber) contain the gbsa.itp file, and one (charmm27), contains a 
gb.itp file.  They all have the same column titles (sar, st, pi, gbr, and hct). 
 I have read the six articles listed at 
http://www.gromacs.org/Documentation/Terminology/Implicit_Solvent, however I 
still have the following two questions regarding the contents of this file:

(1.)  What values are tabulated in these columns and what are the corresponding 
references for each of them?
(2.)  Which columns are used (versus ignored) by Gromacs in the implementation 
of each of the methods (Still/HCT/OBC)?

Here are my guesses for Question 1:
(a.)  sar: solvent accessible surface area?
(b.)  st: surface tension?
(c.)  pi: ?
(d.)  gbr: generalized born radius?  These values correspond to sigma/2 from 
Jorgensen and Tirado-Rives' 1988 JACS paper (v. 110, p. 1657).  However the 
generalized born radius is equal to Rvdw plus a dielectric offset distance, 
according to Still et al's 1997 J. Phys. Chem. A paper (v. 101, p. 3005).  This 
would mean the dielectric offset distance is set to zero (?).  
(e.)  hct: HCT parameter

With an eventual goal of implementing implicit solvent using my lab's force 
field, insight into the meaning of the columns and/or references for their 
origin would be greatly appreciated. 

Thanks in advance! 

Sincerely yours,

E. A. Ploetz
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Re: [gmx-users] g_dist issue( Out put file)

2010-08-23 Thread teklebrh 

Dear Justine,
Reading file PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr, VERSION 3.3.3  
(single precision)

Group 0 (  System) has 28708 elements
Group 1 ( PAP) has   512 elements
Group 2 ( HEP) has 28196 elements
Group 3 (RING) has20 elements
Select a group: 3
Selected 3: 'RING'
Select a group: 3
Selected 3: 'RING'
Reading frame   0 time 19000.000
Back Off! I just backed up DistPAP8HEP.xvg to ./#DistPAP8HEP.xvg.8#
Last frame500 time 2.000



which means I have to create two index file for two rings Ring_1 AND  
Ring_2 and choose both of them. If I am correct.


Rob




Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

The following is the out put.

# This file was created Mon Aug 23 11:18:45 2010
# by the following command:
# /home/software/gromacs/3.3.3/bin/g_dist -f  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2  
-o DistPAP8HEP.xvg

#
# /home/software/gromacs/3.3.3/bin/g_dist is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.0000.0000.0000.000
19002.0000.0000.0000.0000.000
19004.0000.0000.0000.0000.000
19006.0000.0000.0000.0000.000
19008.0000.0000.0000.0000.000
19010.0000.0000.0000.0000.000
19012.0000.0000.0000.0000.000
19014.0000.0000.0000.0000.000
19016.0000.0000.0000.0000.000
19018.0000.0000.0000.0000.000
19020.0000.0000.0000.0000.000
19022.0000.0000.0000.0000.000
19024.0000.0000.0000.0000.000
19026.0000.0000.0000.0000.000
19028.0000.0000.0000.0000.000
19030.0000.0000.0000.0000.000
19032.0000.0000.0



You say you want the distance between two rings, but you only showed  
an index group for one of them (presumably), and the fact that  
you've gotten all zeroes as a result would suggest that you chose  
the same group twice for the distance calculation.  Which groups did  
you select?  Do they correspond to two, non-overlapping index groups?


-Justin




Quoting tekle...@ualberta.ca:


Dear Gromacs users,

I run my simulation for 20ns and want to extract aromatic-aromatic  
distance to see the stacking issue. But I am unable to get the  
value.


I have 24 molecules in my simulation and filled with solvents.

My index file is like that:

[ System ]
  123456789   10   11   12   13   14   15
 16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
 31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
 46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
 61   62
 '''
 '''
 '''
 ''

[ RING ]
 19   20   21   22   23   24   25   26   27   28   29   30
 32   34   37   38   39   40   42   44

This is the ring I created plane in the index file.

I used this command line

g_dist -f PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2  
-o DistPAP8HEP.xvg


but got the following like

I want to get the mean separation distance between two consecutive  
polyaromatic rings along the axis of stacking


can someone help.

rob



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--


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


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Re: [gmx-users] g_dist issue( Out put file)

2010-08-23 Thread Justin A. Lemkul 



tekle...@ualberta.ca wrote:

Dear Justine,
Reading file PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr, VERSION 3.3.3 (single 
precision)

Group 0 (  System) has 28708 elements
Group 1 ( PAP) has   512 elements
Group 2 ( HEP) has 28196 elements
Group 3 (RING) has20 elements
Select a group: 3
Selected 3: 'RING'
Select a group: 3
Selected 3: 'RING'
Reading frame   0 time 19000.000
Back Off! I just backed up DistPAP8HEP.xvg to ./#DistPAP8HEP.xvg.8#
Last frame500 time 2.000



which means I have to create two index file for two rings Ring_1 AND 
Ring_2 and choose both of them. If I am correct.




Yes.  Otherwise the distance from the center of mass of RING is calculated 
relative to the center of mass of RING, which by definition will always be zero.


-Justin


Rob




Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

The following is the out put.

# This file was created Mon Aug 23 11:18:45 2010
# by the following command:
# /home/software/gromacs/3.3.3/bin/g_dist -f 
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s 
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2 -o 
DistPAP8HEP.xvg

#
# /home/software/gromacs/3.3.3/bin/g_dist is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.0000.0000.0000.000
19002.0000.0000.0000.0000.000
19004.0000.0000.0000.0000.000
19006.0000.0000.0000.0000.000
19008.0000.0000.0000.0000.000
19010.0000.0000.0000.0000.000
19012.0000.0000.0000.0000.000
19014.0000.0000.0000.0000.000
19016.0000.0000.0000.0000.000
19018.0000.0000.0000.0000.000
19020.0000.0000.0000.0000.000
19022.0000.0000.0000.0000.000
19024.0000.0000.0000.0000.000
19026.0000.0000.0000.0000.000
19028.0000.0000.0000.0000.000
19030.0000.0000.0000.0000.000
19032.0000.0000.0



You say you want the distance between two rings, but you only showed 
an index group for one of them (presumably), and the fact that you've 
gotten all zeroes as a result would suggest that you chose the same 
group twice for the distance calculation.  Which groups did you 
select?  Do they correspond to two, non-overlapping index groups?


-Justin




Quoting tekle...@ualberta.ca:


Dear Gromacs users,

I run my simulation for 20ns and want to extract aromatic-aromatic 
distance to see the stacking issue. But I am unable to get the value.


I have 24 molecules in my simulation and filled with solvents.

My index file is like that:

[ System ]
  123456789   10   11   12   13   
14   15
 16   17   18   19   20   21   22   23   24   25   26   27   28   
29   30
 31   32   33   34   35   36   37   38   39   40   41   42   43   
44   45
 46   47   48   49   50   51   52   53   54   55   56   57   58   
59   60

 61   62
 '''
 '''
 '''
 ''

[ RING ]
 19   20   21   22   23   24   25   26   27   28   29   30
 32   34   37   38   39   40   42   44

This is the ring I created plane in the index file.

I used this command line

g_dist -f PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s 
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2 
-o DistPAP8HEP.xvg


but got the following like

I want to get the mean separation distance between two consecutive 
polyaromatic rings along the axis of stacking


can someone help.

rob



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


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Pleas

Re: [gmx-users] GB Parameters

2010-08-23 Thread David van der Spoel 

On 2010-08-23 19.27, Elizabeth Ploetz wrote:

Dear Gromacs Users,

I am interested in implementing implicit solvent using the OBC GBSA method.  In 
the Gromacs 4.5beta3 top directory, several force fields (oplsaa and multiple 
versions of amber) contain the gbsa.itp file, and one (charmm27), contains a 
gb.itp file.  They all have the same column titles (sar, st, pi, gbr, and hct). 
 I have read the six articles listed at 
http://www.gromacs.org/Documentation/Terminology/Implicit_Solvent, however I 
still have the following two questions regarding the contents of this file:

(1.)  What values are tabulated in these columns and what are the corresponding 
references for each of them?
(2.)  Which columns are used (versus ignored) by Gromacs in the implementation 
of each of the methods (Still/HCT/OBC)?

Here are my guesses for Question 1:
(a.)  sar: solvent accessible surface area?
(b.)  st: surface tension?
(c.)  pi: ?
(d.)  gbr: generalized born radius?  These values correspond to sigma/2 from 
Jorgensen and Tirado-Rives' 1988 JACS paper (v. 110, p. 1657).  However the 
generalized born radius is equal to Rvdw plus a dielectric offset distance, 
according to Still et al's 1997 J. Phys. Chem. A paper (v. 101, p. 3005).  This 
would mean the dielectric offset distance is set to zero (?).
(e.)  hct: HCT parameter

With an eventual goal of implementing implicit solvent using my lab's force 
field, insight into the meaning of the columns and/or references for their 
origin would be greatly appreciated.

Thanks in advance!

Sincerely yours,

E. A. Ploetz

Hi Elizabeth,

I can not answer your question, but it is very good that you are 
scrutinizing this stuff, since it is new code...


Does your lab's force field include support for nucleic acids? This is 
missing from the current Charmm implementation although there are 
rumours that parameters exist.



--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] GB Parameters

2010-08-23 Thread Per Larsson 
Hi!

Values in columns 1-3 are not currently used in version beta3. They pertain to 
more elaborate surface area algorithms, the one from Still et al in particular.

Column 4 is the Vdw-radii for atom types that are used for computing the Born 
radii. The dielectric offset is specified in the mdp-file, and gets added to 
the input radii for the different radii methods.

Column 5 is the scale factor for the HCT/OBC models. The values are taken from 
the original HCT reference, as well as the corresponding implementation in 
Tinker. 

/Per

23 aug 2010 kl. 19:27 skrev Elizabeth Ploetz :

> Dear Gromacs Users, 
> 
> I am interested in implementing implicit solvent using the OBC GBSA method.  
> In the Gromacs 4.5beta3 top directory, several force fields (oplsaa and 
> multiple versions of amber) contain the gbsa.itp file, and one (charmm27), 
> contains a gb.itp file.  They all have the same column titles (sar, st, pi, 
> gbr, and hct).  I have read the six articles listed at 
> http://www.gromacs.org/Documentation/Terminology/Implicit_Solvent, however I 
> still have the following two questions regarding the contents of this file:
> 
> (1.)  What values are tabulated in these columns and what are the 
> corresponding references for each of them?
> (2.)  Which columns are used (versus ignored) by Gromacs in the 
> implementation of each of the methods (Still/HCT/OBC)?
> 
> Here are my guesses for Question 1:
> (a.)  sar: solvent accessible surface area?
> (b.)  st: surface tension?
> (c.)  pi: ?
> (d.)  gbr: generalized born radius?  These values correspond to sigma/2 from 
> Jorgensen and Tirado-Rives' 1988 JACS paper (v. 110, p. 1657).  However the 
> generalized born radius is equal to Rvdw plus a dielectric offset distance, 
> according to Still et al's 1997 J. Phys. Chem. A paper (v. 101, p. 3005).  
> This would mean the dielectric offset distance is set to zero (?).  
> (e.)  hct: HCT parameter
> 
> With an eventual goal of implementing implicit solvent using my lab's force 
> field, insight into the meaning of the columns and/or references for their 
> origin would be greatly appreciated. 
> 
> Thanks in advance! 
> 
> Sincerely yours,
> 
> E. A. Ploetz
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
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Re: [gmx-users] g_dist issue( Out put file)

2010-08-23 Thread teklebrh 

Dear Justine,

I got it and works fine.

@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.7047197   -0.3054392   -0.15599120.6156325
19002.0000.7591453   -0.2601027   -0.26593630.6617599
19004.0000.7763510   -0.3043177   -0.22149120.6790090
19006.0000.7837191   -0.2325068   -0.26536930.6998110
=

I have another question for you. Does g_analyse is oky to use to get  
the mean separation.


g_anayze -f .xvg -av average.xvg -errbar enum -b 19000 -e 2

is the column 1 and two is correct means time and distance respectively.

=


Is the same process apply for the g-rdf?

 Group 0 (  System) has 28708 elements

Group 1 ( PAP) has   512 elements
Group 2 ( HEP) has 28196 elements
Group 3 (RING) has20 elements


I want to calculate g(r) for PAP molecules.. but by default it is  
there does I need to create two PAP_1 and PAP_2 to get the g(r). To  
get for the


PAP-PAP g(r) value. Or just need to select 1 twice?

Rob


Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

Dear Justine,
Reading file PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr, VERSION 3.3.3  
(single precision)

Group 0 (  System) has 28708 elements
Group 1 ( PAP) has   512 elements
Group 2 ( HEP) has 28196 elements
Group 3 (RING) has20 elements
Select a group: 3
Selected 3: 'RING'
Select a group: 3
Selected 3: 'RING'
Reading frame   0 time 19000.000
Back Off! I just backed up DistPAP8HEP.xvg to ./#DistPAP8HEP.xvg.8#
Last frame500 time 2.000



which means I have to create two index file for two rings Ring_1  
AND Ring_2 and choose both of them. If I am correct.




Yes.  Otherwise the distance from the center of mass of RING is  
calculated relative to the center of mass of RING, which by  
definition will always be zero.


-Justin


Rob




Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

The following is the out put.

# This file was created Mon Aug 23 11:18:45 2010
# by the following command:
# /home/software/gromacs/3.3.3/bin/g_dist -f  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s  
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e  
2 -o DistPAP8HEP.xvg

#
# /home/software/gromacs/3.3.3/bin/g_dist is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.0000.0000.0000.000
19002.0000.0000.0000.0000.000
19004.0000.0000.0000.0000.000
19006.0000.0000.0000.0000.000
19008.0000.0000.0000.0000.000
19010.0000.0000.0000.0000.000
19012.0000.0000.0000.0000.000
19014.0000.0000.0000.0000.000
19016.0000.0000.0000.0000.000
19018.0000.0000.0000.0000.000
19020.0000.0000.0000.0000.000
19022.0000.0000.0000.0000.000
19024.0000.0000.0000.0000.000
19026.0000.0000.0000.0000.000
19028.0000.0000.0000.0000.000
19030.0000.0000.0000.0000.000
19032.0000.0000.0



You say you want the distance between two rings, but you only  
showed an index group for one of them (presumably), and the fact  
that you've gotten all zeroes as a result would suggest that you  
chose the same group twice for the distance calculation.  Which  
groups did you select?  Do they correspond to two, non-overlapping  
index groups?


-Justin




Quoting tekle...@ualberta.ca:


Dear Gromacs users,

I run my simulation for 20ns and want to extract  
aromatic-aromatic distance to see the stacking issue. But I am  
unable to get the value.


I have 24 molecules in my simulation and filled with solvents.

My index file is like that:

[ System ]
 123456789   10   11   12   13   14   15
16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
61   62
'''
'''
'''
''

[ RING ]
19   20   21   22   23   24   25   26   27   28   29   30
32   34   37   38   39   40   42   44

This is the ring I c

Re: [gmx-users] g_dist issue( Out put file)

2010-08-23 Thread Justin A. Lemkul 



tekle...@ualberta.ca wrote:

Dear Justine,

I got it and works fine.

@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.7047197   -0.3054392   -0.15599120.6156325
19002.0000.7591453   -0.2601027   -0.26593630.6617599
19004.0000.7763510   -0.3043177   -0.22149120.6790090
19006.0000.7837191   -0.2325068   -0.26536930.6998110
=

I have another question for you. Does g_analyse is oky to use to get the 
mean separation.




I don't see why not.  That's pretty much the main function of g_analyze.


g_anayze -f .xvg -av average.xvg -errbar enum -b 19000 -e 2

is the column 1 and two is correct means time and distance respectively.



Per the notation in the .xvg file, yes.


=


Is the same process apply for the g-rdf?

 Group 0 (  System) has 28708 elements

Group 1 ( PAP) has   512 elements
Group 2 ( HEP) has 28196 elements
Group 3 (RING) has20 elements


I want to calculate g(r) for PAP molecules.. but by default it is 
there does I need to create two PAP_1 and PAP_2 to get the g(r). To get 
for the


PAP-PAP g(r) value. Or just need to select 1 twice?


Try it and see :)

-Justin



Rob


Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

Dear Justine,
Reading file PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr, VERSION 3.3.3 
(single precision)

Group 0 (  System) has 28708 elements
Group 1 ( PAP) has   512 elements
Group 2 ( HEP) has 28196 elements
Group 3 (RING) has20 elements
Select a group: 3
Selected 3: 'RING'
Select a group: 3
Selected 3: 'RING'
Reading frame   0 time 19000.000
Back Off! I just backed up DistPAP8HEP.xvg to ./#DistPAP8HEP.xvg.8#
Last frame500 time 2.000



which means I have to create two index file for two rings Ring_1 AND 
Ring_2 and choose both of them. If I am correct.




Yes.  Otherwise the distance from the center of mass of RING is 
calculated relative to the center of mass of RING, which by definition 
will always be zero.


-Justin


Rob




Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

The following is the out put.

# This file was created Mon Aug 23 11:18:45 2010
# by the following command:
# /home/software/gromacs/3.3.3/bin/g_dist -f 
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s 
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2 
-o DistPAP8HEP.xvg

#
# /home/software/gromacs/3.3.3/bin/g_dist is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.0000.0000.0000.000
19002.0000.0000.0000.0000.000
19004.0000.0000.0000.0000.000
19006.0000.0000.0000.0000.000
19008.0000.0000.0000.0000.000
19010.0000.0000.0000.0000.000
19012.0000.0000.0000.0000.000
19014.0000.0000.0000.0000.000
19016.0000.0000.0000.0000.000
19018.0000.0000.0000.0000.000
19020.0000.0000.0000.0000.000
19022.0000.0000.0000.0000.000
19024.0000.0000.0000.0000.000
19026.0000.0000.0000.0000.000
19028.0000.0000.0000.0000.000
19030.0000.0000.0000.0000.000
19032.0000.0000.0



You say you want the distance between two rings, but you only showed 
an index group for one of them (presumably), and the fact that 
you've gotten all zeroes as a result would suggest that you chose 
the same group twice for the distance calculation.  Which groups did 
you select?  Do they correspond to two, non-overlapping index groups?


-Justin




Quoting tekle...@ualberta.ca:


Dear Gromacs users,

I run my simulation for 20ns and want to extract aromatic-aromatic 
distance to see the stacking issue. But I am unable to get the value.


I have 24 molecules in my simulation and filled with solvents.

My index file is like that:

[ System ]
 123456789   10   11   12   13   
14   15
16   17   18   19   20   21   22   23   24   25   26   27   28   
29   30
31   32   33   34   35   36   37   38   39   40   41   42   43   
44   45
46   47   48   49   50   51   52   53   54   55   56   57   58   
59   6

Re: [gmx-users] Does anyone know how to get the file charmm_gromacs.tar.gz?

2010-08-23 Thread fang yuan 
Hi, I have the same problem, I need to implement the general CHARMM
forcefield in gromacs, so I need to know how to convert the rtf files into
rtp files in gromacs

On Sun, Aug 22, 2010 at 10:11 AM, David van der Spoel
wrote:

> On 2010-08-22 15.16, Michael McGovern wrote:
>
>> I'm looking for an rtp file for charmm in gromacs and according to
>> http://www.gromacs.org/Downloads/User_contributions/Other_software
>> It should be available in a file called charmm_gromacs.tar.gz at
>>
>> http://www.gromacs.org/old/topologies/uploaded_force_fields/charmm_gromacs.tar.gz
>> <
>> http://www.gromacs.org/old/topologies/uploaded_force_fields/charmm_gromacs.tar.gz
>>  >
>> but the link is broken and just leads to the main gromacs web page. Does
>> anyone know where I can find this file, or maybe you have it yourself?
>> Thanks a lot.
>>
>>
>>  Try the 4.5beta. It contains the charmm ff.
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> or send it to gmx-users-requ...@gromacs.org.
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>
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Re: [gmx-users] GB Parameters

2010-08-23 Thread Per Larsson 
Also, again, as David said, if you find any errors in the parameters or in the 
code, please let me know!

Cheers
/Per


23 aug 2010 kl. 20:09 skrev Per Larsson :

> Hi!
> 
> Values in columns 1-3 are not currently used in version beta3. They pertain 
> to more elaborate surface area algorithms, the one from Still et al in 
> particular.
> 
> Column 4 is the Vdw-radii for atom types that are used for computing the Born 
> radii. The dielectric offset is specified in the mdp-file, and gets added to 
> the input radii for the different radii methods.
> 
> Column 5 is the scale factor for the HCT/OBC models. The values are taken 
> from the original HCT reference, as well as the corresponding implementation 
> in Tinker. 
> 
> /Per
> 
> 23 aug 2010 kl. 19:27 skrev Elizabeth Ploetz :
> 
>> Dear Gromacs Users, 
>> 
>> I am interested in implementing implicit solvent using the OBC GBSA method.  
>> In the Gromacs 4.5beta3 top directory, several force fields (oplsaa and 
>> multiple versions of amber) contain the gbsa.itp file, and one (charmm27), 
>> contains a gb.itp file.  They all have the same column titles (sar, st, pi, 
>> gbr, and hct).  I have read the six articles listed at 
>> http://www.gromacs.org/Documentation/Terminology/Implicit_Solvent, however I 
>> still have the following two questions regarding the contents of this file:
>> 
>> (1.)  What values are tabulated in these columns and what are the 
>> corresponding references for each of them?
>> (2.)  Which columns are used (versus ignored) by Gromacs in the 
>> implementation of each of the methods (Still/HCT/OBC)?
>> 
>> Here are my guesses for Question 1:
>> (a.)  sar: solvent accessible surface area?
>> (b.)  st: surface tension?
>> (c.)  pi: ?
>> (d.)  gbr: generalized born radius?  These values correspond to sigma/2 from 
>> Jorgensen and Tirado-Rives' 1988 JACS paper (v. 110, p. 1657).  However the 
>> generalized born radius is equal to Rvdw plus a dielectric offset distance, 
>> according to Still et al's 1997 J. Phys. Chem. A paper (v. 101, p. 3005).  
>> This would mean the dielectric offset distance is set to zero (?).  
>> (e.)  hct: HCT parameter
>> 
>> With an eventual goal of implementing implicit solvent using my lab's force 
>> field, insight into the meaning of the columns and/or references for their 
>> origin would be greatly appreciated. 
>> 
>> Thanks in advance! 
>> 
>> Sincerely yours,
>> 
>> E. A. Ploetz
>> -- 
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the 
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Charmm to Gromacs: Polyols force field [Justin]

2010-08-23 Thread Bruce D. Ray 
On Mon, August 23, 2010 12:12 PM, Eudes Fileti  wrote:

> Well, the line 40 is just one of the 36 parameters not found!
> In this link ( https://sites.google.com/site/fileti/ ) I put
> the complete files. 
> I know I need to determine which bond type should be called
> and I believe that it has been done, but I don't know why
> it's not being found.

Well, I'm not Justin, but as I look at your topology, I see
that you have a bond from atom 3, type CC322, to atom 6,
also type CC322.  However, when I look at the parameters you
give in the bondtypes section, I cannot find a CC322  CC322
bond defined.  Either the entry is missing or you did not
post a complete set of force field entries.

Missing entries might be the cause of theother parameters
not found as well, which is what was suggested to you
previously.


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



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Re: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Mark, Justin]

2010-08-23 Thread Eudes Fileti 
Olá,
Mark and Justin.
Solved.
I did what you suggested and I got all the default values.

Muito obrigado!
eef

___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4996-0196
http://fileti.ufabc.edu.br
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Re: [gmx-users] Does anyone know how to get the file charmm_gromacs.tar.gz?

2010-08-23 Thread Mark Abraham 


- Original Message -
From: fang yuan 
Date: Tuesday, August 24, 2010 4:52
Subject: Re: [gmx-users] Does anyone know how to get the file 
charmm_gromacs.tar.gz?
To: Discussion list for GROMACS users 

> Hi, I have the same problem, I need to implement the general CHARMM 
> forcefield in gromacs, so I need to know how to convert the rtf files into 
> rtp files in gromacs

There's never been an automated tool for that.

Mark

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