[gmx-users] Distance restraint energy terms

[nikhil damle]

Hi,

I have applied distance restraints on my system during MD simulation through 
following options:
"disre = simple" and disre_fc = 2000 in .mdp file.
Now i wish to see the energy term corresponding to these restraints in 
principle to be written in .edr file. But g_energy programme does not list any 
term corresponding to these restraints. 

I have following 2 questions:
1. How one should ensure that the restraints are applied correctly ?
2. How should I check the corresponding energy ? 

Plz help ASAP

Regards,
Nikhil


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Re: [gmx-users] Compiling 4.0.7 parallel fails

[Chandan Choudhury]

I had also had trouble installing gmx (paralley). But now, its solved.
I would suggest you to see that the mpi is running or not.
Here is a sample mpi C program:

#include 
#include "mpi.h"

int main( argc, argv )
int  argc;
char **argv;
{
int rank, size;
MPI_Init( &argc, &argv );
MPI_Comm_size( MPI_COMM_WORLD, &size );
MPI_Comm_rank( MPI_COMM_WORLD, &rank );
printf( "Hello world from process %d of %d\n", rank, size );
MPI_Finalize();
return 0;
}

save as mpitest.c
compile mpitest.c

mpirun -np 2 -machilefile mac a.out

If every thing is ok. Then the output will be :

Hello world from process


Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Sat, Feb 6, 2010 at 5:47 AM, Jussi Lehtola wrote:

> On Fri, 2010-02-05 at 15:29 -0500, Matthew L. Danielson wrote:
> > Compiling fftw and openmpi seems to finish successfully.  The serial
> > version of gromacs installed correctly, just when i issue --enable-mpi i
> > am seeing this error message (i can attached the config.log if it would
> > help):
> > "checking size of int... configure: error: cannot compute sizeof (int)"
> >
> >  From what i can get out of the mail-archive, I think this is  problem
> > with the mpi installation or not finding the correct files etc.  I have
> > tried re-installing openmpi (always removing the old version) using yum
> > (installed version 1.3.2) and installing openmpi from their website
> > (1.4.1).  Both seem to install correctly, yet the same error message
> > arises when i do ./configure --enable-mpi for gromacs.
>
> What distribution are you using? If you are running Fedora 12, you need
> to load the MPI environment module with e.g.
>  $ module load openmpi-x86_64
>
> Furthermore, you should have the fftw-devel and openmpi-devel packages
> installed on your system.
> --
> --
> Jussi Lehtola, FM, Tohtorikoulutettava
> Fysiikan laitos, Helsingin Yliopisto
> jussi.leht...@helsinki.fi, p. 191 50632
> --
> Mr. Jussi Lehtola, M. Sc., Doctoral Student
> Department of Physics, University of Helsinki, Finland
> jussi.leht...@helsinki.fi
> --
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
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Re: [gmx-users] What is demux.pl script

[Mark Abraham]

On 02/06/10, zuole   wrote:



Hello,
 
I've been reading all of the archived questions on the analysis of REMD in Gromacs, and I'm still a bit confused. It appears that the first step is to use the demux.pl script to demultiplex the REMD trajectories. That depends on the kind of analysis you wish to perform. If you want trajectories that are structurally continuous but ensemble-discontinuous, use demux.pl. The trajectories written normally are the opposite.MarkHowever, I am unable to find this demux.pl file in the src/contrib/script/ folder. Can anyone please help me out on this? I would really want to know where to find the script or what the content is. 
 
Thanks,
 
Jackie 		 	   		  Hotmail: 免费、可靠、丰富的电子邮件服务。 立即获取。

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Re: [gmx-users] What is demux.pl script

[Justin A. Lemkul]

zuole wrote:

Hello,
 
I've been reading all of the archived questions on the analysis of REMD 
in Gromacs, and I'm still a bit confused. It appears that the first step 
is to use the demux.pl script to demultiplex the REMD trajectories. 
However, I am unable to find this demux.pl file in 
the src/contrib/script/ folder. Can anyone please help me out on this? I 
would really want to know where to find the script or what the content is. 
 


The demux.pl script is in the /bin subdirectory of your Gromacs installation 
(like all the other executables).  The input is a .log file from an REMD run; 
the output is then fed to trjcat when demultiplexing the trajectories.


-Justin


Thanks,
 
Jackie



Hotmail: 免费、可靠、丰富的电子邮件服务。 立即获取。 





--


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] What is demux.pl script

[zuole]

Hello,

 

I've been reading all of the archived questions on the analysis of REMD in 
Gromacs, and I'm still a bit confused. It appears that the first step is to use 
the demux.pl script to demultiplex the REMD trajectories. However, I am unable 
to find this demux.pl file in the src/contrib/script/ folder. Can anyone please 
help me out on this? I would really want to know where to find the script or 
what the content is. 

 

Thanks,

 

Jackie
  
_
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[gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field

[fairuz zulkifli]

to create itp file with OPLS force feild, you can try use GAMESS.
-fairuz-
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Re: [gmx-users] Compiling 4.0.7 parallel fails

[Jussi Lehtola]

On Fri, 2010-02-05 at 15:29 -0500, Matthew L. Danielson wrote:
> Compiling fftw and openmpi seems to finish successfully.  The serial 
> version of gromacs installed correctly, just when i issue --enable-mpi i 
> am seeing this error message (i can attached the config.log if it would 
> help):
> "checking size of int... configure: error: cannot compute sizeof (int)"
> 
>  From what i can get out of the mail-archive, I think this is  problem 
> with the mpi installation or not finding the correct files etc.  I have 
> tried re-installing openmpi (always removing the old version) using yum 
> (installed version 1.3.2) and installing openmpi from their website 
> (1.4.1).  Both seem to install correctly, yet the same error message 
> arises when i do ./configure --enable-mpi for gromacs.

What distribution are you using? If you are running Fedora 12, you need
to load the MPI environment module with e.g.
 $ module load openmpi-x86_64

Furthermore, you should have the fftw-devel and openmpi-devel packages
installed on your system.
-- 
--
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.leht...@helsinki.fi, p. 191 50632
--
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.leht...@helsinki.fi
--


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Re: [gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field

[Bruce D. Ray]

On Fri, February 5, 2010 at 1:06:34 PM, Antoine Delmotte 

wrote:

> I would like to simulate the CDK9 protein (3BLH in PDB), but there is
one residue (TPO,
> phosphothreonine), which Gromacs does not recognise.
> 
> I
found the PRODRG website as well as force field parameters for TPO for
the Gromos96.1
> force field. However, I would like to use the OPLS-AA
force field. I therefore need a topology
> file for this force field,
which cannot be provided by PRODRG (only useful for united atoms
> force
fields).
> 
> Does anyone have an idea about where I could get the phosphothreonine itp 
> file for OPLS
> force field?
> 
> Otherwise, could someone give me clues or the link to a good tutorial about 
> how to create
> this itp file myself? 
> 
> Molecular
dynamics is something completely new for me so, sorry if I ask stupid
questions.
> It also seems I am not the first one to have this problem
but I could not find any solution on
> the archive of the mailing list.

The charges probably need a little more work, but this might be a start towards 
an
rtp file for phosphothreonine to add to ffoplsaa.rtp.

[ TPO ]
 [ atoms ]
 Nopls_238   -0.500 1
 Hopls_2410.300 1
CAopls_224B   0.140 1
HAopls_1400.060 1
CBopls_1580.205 2
HBopls_1400.060 2
   OG1opls_447   -0.700 2
 Popls_4451.795 3
   O1Popls_446   -1.120 3
   O2Popls_446   -1.120 3
   O3Popls_446   -1.120 3
   CG2opls_135   -0.180 4
  HG21opls_1400.060 4
  HG22opls_1400.060 4
  HG23opls_1400.060 4
 Copls_2350.500 5
 Oopls_236   -0.500 5
 [ bonds ]
 N H
 NCA
CAHA
CACB
CA C
CBHB
CB   OG1
CB   CG2
   OG1 P
   O1P P
   O2P P
   O3P P
   CG2  HG21
   CG2  HG22
   CG2  HG23
 C O
-C N
 [ dihedrals ] ; override some of the typebased dihedrals
 NCACB   OG1dih_SER_THR_chi1_N_C_C_O
 CCACB   OG1dih_SER_THR_chi1_CO_C_C_O
CACB   OG1   HG1dih_SER_THR_chi2_C_C_OH_HO
 [ impropers ]
-CCA N Himproper_Z_N_X_Y 
CA+N C Oimproper_O_C_X_Y 


I hope that helps.


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



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Re: [gmx-users] segmentation fault with grompp

[Justin A. Lemkul]

Gard Nelson wrote:

Hi all,
I'm trying to simulate a solvated membrane using Berger's lipids.  When 
I run grompp, i get the following error:


checking input for internal consistency...
processing topology...
Opening library file ...lipid.itp
Opening library file ...nb_lipid.itp
Opening library file ...bon_lipid.itp
Opening library file ...ff_dum.itp
Segmentation fault (core dumped)

I've tried this on two different machines with two different ff_dum.itp 
files with the same results. Moreover, I've never touched the ff_dum.itp 
file.  I have modified the other forcefield files, both to include 
Berger's lipids as well as other non-standard residues.  It runs fine 
with solvated proteins, but this is the first time I've run a system 
with the membrane, so i'm guessing the error is coming from there.  I've 
looked through my files and cant find any errors.  Does anyone have any 
ideas of what might be causing this?




Lots of things.  But to get better help, you'll have to provide some more 
information:


1. Gromacs version
2. Platform
3. How Gromacs was compiled (commands, compilers used, etc)

-Justin


Thanks
Gard Nelson



--


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] segmentation fault with grompp

[Gard Nelson]

Hi all,
I'm trying to simulate a solvated membrane using Berger's lipids.  When I
run grompp, i get the following error:

checking input for internal consistency...
processing topology...
Opening library file ...lipid.itp
Opening library file ...nb_lipid.itp
Opening library file ...bon_lipid.itp
Opening library file ...ff_dum.itp
Segmentation fault (core dumped)

I've tried this on two different machines with two different ff_dum.itp
files with the same results. Moreover, I've never touched the ff_dum.itp
file.  I have modified the other forcefield files, both to include Berger's
lipids as well as other non-standard residues.  It runs fine with solvated
proteins, but this is the first time I've run a system with the membrane, so
i'm guessing the error is coming from there.  I've looked through my files
and cant find any errors.  Does anyone have any ideas of what might be
causing this?

Thanks
Gard Nelson
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Re: Fwd: [gmx-users] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds

[Justin A. Lemkul]

Vitaly V. Chaban wrote:

Yes, I provided all the possible entries in the N2T.although the
problem is the same. I also recreated PDB and re-measured the
distances but everything seems pretty correct in my PDB.

N   N 2   S  0.17 S 0.17
F   F 1   C  0.14
S   S 4   O  0.17 O 0.17 C 0.18  N 0.17
C   C 4   F  0.14 F 0.14 F 0.14  S 0.18
O   O 1   S  0.17



Is this to be used with the original .pdb file you posted?  I ran it through and 
it failed with a very important (I think) error:


"There are 0 name to type translations"

As before, the format of your .n2t file is incorrect.  Build a suitable file and 
try again.


-Justin



Vitaly



On Fri, Feb 5, 2010 at 10:13 PM, Justin A. Lemkul  wrote:


Vitaly V. Chaban wrote:

On Fri, Feb 5, 2010 at 9:13 PM, Justin A. Lemkul  wrote:

Vitaly V. Chaban wrote:

In this context, it is interesting how X2TOP decides that two atoms
are connected? Only on the base of N2T: if the atom should have 4
neighbours, it looks for the appropriate number of them?


That's correct.


Then the interesting error is:
"Fatal error:
No forcefield type for atom C (1) with 0 bonds"

while PDB contains other atoms than carbon. If it looks for neighbours
why does not it find them...


The error is complaining that atom 1 (a carbon atom) is not within searching
distance of any atoms to which it should be bonded.  Have you specified .n2t
entries for every one of your atoms?  For example, it is insufficient to
specify an .n2t line for the central S (in your original post) and expect
x2top to understand that the O, N, and C atoms to which it is connected can
have their atom types determined.  You need .n2t entries for all of those
atoms, too, specifying that they are, in turn, connected to S in some way.
 The above error suggests that x2top is finding a carbon atom that you have
not defined in the .n2t file.

-Justin





In my case, maybe it considers that 0.18 nm is too much for two atoms
to be connected?


The length defined in the .n2t file should be the actual bond length
(from
the coordinate file) +/- 10%, like specbond.dat, if I recall; x2top
should
not arbitrarily try to dictate that a bond is too long.

-Justin


-- Forwarded message --
From: Vitaly V. Chaban 
Date: Fri, Feb 5, 2010 at 7:56 PM
Subject: Re: [gmx-users] Re: x2top and bonds. No forcefield type for
atom S (2) with 3 bonds
To: jalem...@vt.edu, gmx-users@gromacs.org


Yes. This worked even with my N2T. I will probably recreate my PDB...


On Fri, Feb 5, 2010 at 7:51 PM, Justin A. Lemkul 
wrote:

Vitaly V. Chaban wrote:

Justin,

Am I correct that X2TOP uses only N2T file to make a topology?


Yes.


I made the full line for Sulphur but it didn't change the situation.
It looks strange that X2TOP notices 3 bonds although I propose to have
4 bonds (and they are present). If I propose 3 bonds, it readily gives
an output... This is like it has predefined Sulphur with 3 bonds.


Certainly not.  Take, for example, a simple SO4 molecule:

REMARK
HETATM1  OAC DRG 1   5.850  14.800 -12.770  1.00 20.00
 O
HETATM2  SAE DRG 1   4.810  15.780 -12.710  1.00 20.00
 S
HETATM3  OAD DRG 1   3.550  15.150 -12.980  1.00 20.00
 O
HETATM4  OAB DRG 1   4.770  16.390 -11.340  1.00 20.00
 O
HETATM5  OAA DRG 1   5.070  16.850 -13.730  1.00 20.00
 O

The topology is generated just fine with this .n2t file:

S   S   0   32.06   4   O  0.145O   0.145   O   0.145   O   0.145
O   OM  0   15.9994 1   S  0.145

I don't know what might be going on with your system, but I would
suggest
creating an .n2t file with only entries pertinent to your system, for
all
atoms involved.  This is, of course, only really useful for debugging,
since
in theory, x2top should be easily extensible by appending the .n2t
file.

-Justin


Vitaly


On Fri, Feb 5, 2010 at 7:18 PM, Vitaly V. Chaban 
wrote:

Hi,

This can be the reason when X2TOP gives the following error:
"
Fatal error:
No forcefield type for atom S (2) with 3 bonds
"
?

I try to translate PDB of the TFSA anion
   OO
   || ||
F3C-S-N-S-CF3
   || ||
   OO

into topology.


My PDB contains optimized geometry:
HEADERTFSA
COMPNDTFSA
AUTHORVVC
ATOM  1  N   TFS 1  -0.000   0.444  -0.008  1.00  0.00
ATOM  2  S   TFS 1   1.401  -0.440  -0.189  1.00  0.00
ATOM  3  S   TFS 1  -1.400  -0.438   0.189  1.00  0.00
ATOM  4  O   TFS 1  -1.236  -1.810  -0.833  1.00  0.00
ATOM  5  O   TFS 1  -1.284  -1.009   1.805  1.00  0.00
ATOM  6  O   TFS 1   1.293  -1.026  -1.800  1.00  0.00
ATOM  7  O   TFS 1   1.233  -1.803   0.845  1.00  0.00
ATOM  8  C   TFS 1  -2.837   0.628  -0.107  1.00  0.00
ATOM  9  C   TFS 1   2.836   0.630   0.105  1.00  0.00
ATOM 10  F   TFS 1  -3.996  -0.097   0.093  1.00  0.00
ATOM 11  F   TFS 1  -2.805   1.094  -1.408  1.00  0.00
ATOM 12  F   TFS 1

Re: Fwd: [gmx-users] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds

[Vitaly V. Chaban]

Yes, I provided all the possible entries in the N2T.although the
problem is the same. I also recreated PDB and re-measured the
distances but everything seems pretty correct in my PDB.

N   N 2   S  0.17 S 0.17
F   F 1   C  0.14
S   S 4   O  0.17 O 0.17 C 0.18  N 0.17
C   C 4   F  0.14 F 0.14 F 0.14  S 0.18
O   O 1   S  0.17


Vitaly



On Fri, Feb 5, 2010 at 10:13 PM, Justin A. Lemkul  wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> On Fri, Feb 5, 2010 at 9:13 PM, Justin A. Lemkul  wrote:
>>>
>>> Vitaly V. Chaban wrote:

 In this context, it is interesting how X2TOP decides that two atoms
 are connected? Only on the base of N2T: if the atom should have 4
 neighbours, it looks for the appropriate number of them?

>>> That's correct.
>>
>>
>> Then the interesting error is:
>> "Fatal error:
>> No forcefield type for atom C (1) with 0 bonds"
>>
>> while PDB contains other atoms than carbon. If it looks for neighbours
>> why does not it find them...
>>
>
> The error is complaining that atom 1 (a carbon atom) is not within searching
> distance of any atoms to which it should be bonded.  Have you specified .n2t
> entries for every one of your atoms?  For example, it is insufficient to
> specify an .n2t line for the central S (in your original post) and expect
> x2top to understand that the O, N, and C atoms to which it is connected can
> have their atom types determined.  You need .n2t entries for all of those
> atoms, too, specifying that they are, in turn, connected to S in some way.
>  The above error suggests that x2top is finding a carbon atom that you have
> not defined in the .n2t file.
>
> -Justin
>
>>
>>
>>
 In my case, maybe it considers that 0.18 nm is too much for two atoms
 to be connected?

>>> The length defined in the .n2t file should be the actual bond length
>>> (from
>>> the coordinate file) +/- 10%, like specbond.dat, if I recall; x2top
>>> should
>>> not arbitrarily try to dictate that a bond is too long.
>>>
>>> -Justin
>>>
 -- Forwarded message --
 From: Vitaly V. Chaban 
 Date: Fri, Feb 5, 2010 at 7:56 PM
 Subject: Re: [gmx-users] Re: x2top and bonds. No forcefield type for
 atom S (2) with 3 bonds
 To: jalem...@vt.edu, gmx-users@gromacs.org


 Yes. This worked even with my N2T. I will probably recreate my PDB...


 On Fri, Feb 5, 2010 at 7:51 PM, Justin A. Lemkul 
 wrote:
>
> Vitaly V. Chaban wrote:
>>
>> Justin,
>>
>> Am I correct that X2TOP uses only N2T file to make a topology?
>>
> Yes.
>
>> I made the full line for Sulphur but it didn't change the situation.
>> It looks strange that X2TOP notices 3 bonds although I propose to have
>> 4 bonds (and they are present). If I propose 3 bonds, it readily gives
>> an output... This is like it has predefined Sulphur with 3 bonds.
>>
> Certainly not.  Take, for example, a simple SO4 molecule:
>
> REMARK
> HETATM    1  OAC DRG     1       5.850  14.800 -12.770  1.00 20.00
>  O
> HETATM    2  SAE DRG     1       4.810  15.780 -12.710  1.00 20.00
>  S
> HETATM    3  OAD DRG     1       3.550  15.150 -12.980  1.00 20.00
>  O
> HETATM    4  OAB DRG     1       4.770  16.390 -11.340  1.00 20.00
>  O
> HETATM    5  OAA DRG     1       5.070  16.850 -13.730  1.00 20.00
>  O
>
> The topology is generated just fine with this .n2t file:
>
> S   S   0   32.06   4   O  0.145    O   0.145   O   0.145   O   0.145
> O   OM  0   15.9994 1   S  0.145
>
> I don't know what might be going on with your system, but I would
> suggest
> creating an .n2t file with only entries pertinent to your system, for
> all
> atoms involved.  This is, of course, only really useful for debugging,
> since
> in theory, x2top should be easily extensible by appending the .n2t
> file.
>
> -Justin
>
>> Vitaly
>>
>>
>> On Fri, Feb 5, 2010 at 7:18 PM, Vitaly V. Chaban 
>> wrote:
>>>
>>> Hi,
>>>
>>> This can be the reason when X2TOP gives the following error:
>>> "
>>> Fatal error:
>>> No forcefield type for atom S (2) with 3 bonds
>>> "
>>> ?
>>>
>>> I try to translate PDB of the TFSA anion
>>>    O    O
>>>    ||     ||
>>> F3C-S-N-S-CF3
>>>    ||     ||
>>>    O    O
>>>
>>> into topology.
>>>
>>>
>>> My PDB contains optimized geometry:
>>> HEADER    TFSA
>>> COMPND    TFSA
>>> AUTHOR    VVC
>>> ATOM      1  N   TFS     1      -0.000   0.444  -0.008  1.00  0.00
>>> ATOM      2  S   TFS     1       1.401  -0.440  -0.189  1.00  0.00
>>> ATOM      3  S   TFS     1      -1.400  -0.438   0.189  1.00  0.00
>>> ATOM      4  O   TFS     1      -1.236  -1.810  -0.833  1.00  0.00
>>> ATOM      5  O   TFS     1      -1.284  -1.009   1.805  1.00  0.00
>>> ATOM      6  O   TFS

[gmx-users] Compiling 4.0.7 parallel fails

[Matthew L. Danielson]

Users,

I am having a problem installing version 4.0.7, specifically the 
parallel version.  Searching the mailing archives i came across several 
posts related to my problem but none seemed to offered a solution to the 
error message i am seeing (tried all suggestions).  I have root access 
to my machine (installing in /usr/local) so there should not be any 
permission problems.


Here is exactly what i have done (tried to follow the instructions on 
the website but i find this section not as well put together on the new 
site):

1.  fftw-3.3.1: ./configure --enable-float, make -j 4, make install
2.  openmpi-1.2.8: ./configure, make -j 4, make install
3.  gromacs-4.0.7: ./configure --enable-mpi

Compiling fftw and openmpi seems to finish successfully.  The serial 
version of gromacs installed correctly, just when i issue --enable-mpi i 
am seeing this error message (i can attached the config.log if it would 
help):

"checking size of int... configure: error: cannot compute sizeof (int)"

From what i can get out of the mail-archive, I think this is  problem 
with the mpi installation or not finding the correct files etc.  I have 
tried re-installing openmpi (always removing the old version) using yum 
(installed version 1.3.2) and installing openmpi from their website 
(1.4.1).  Both seem to install correctly, yet the same error message 
arises when i do ./configure --enable-mpi for gromacs.


I have also tried to set in my bash shell:  export 
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/openmpi-1.2.8/ompi/.libs:/usr/local/lib.  
Same problem still as above.


Anyone had this problem and solved it?  Or can anyone possible offer a 
solution?  I am to the point where i do not know where to look next & I 
would appreciate any feedback.


Thanks,
Matt Danielson

--

Matthew L. Danielson

Graduate Student of Medicinal Chemistry & Molecular Pharmacology
College of Pharmacy, Nursing, and Health Sciences
Purdue University
MCMP RHPH 504c
575 Stadium Mall Drive
West Lafayette, IN 47907-2091

(765)496-6643 office 


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Re: Fwd: [gmx-users] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds

[Justin A. Lemkul]

Vitaly V. Chaban wrote:

On Fri, Feb 5, 2010 at 9:13 PM, Justin A. Lemkul  wrote:


Vitaly V. Chaban wrote:

In this context, it is interesting how X2TOP decides that two atoms
are connected? Only on the base of N2T: if the atom should have 4
neighbours, it looks for the appropriate number of them?


That's correct.



Then the interesting error is:
"Fatal error:
No forcefield type for atom C (1) with 0 bonds"

while PDB contains other atoms than carbon. If it looks for neighbours
why does not it find them...



The error is complaining that atom 1 (a carbon atom) is not within searching 
distance of any atoms to which it should be bonded.  Have you specified .n2t 
entries for every one of your atoms?  For example, it is insufficient to specify 
an .n2t line for the central S (in your original post) and expect x2top to 
understand that the O, N, and C atoms to which it is connected can have their 
atom types determined.  You need .n2t entries for all of those atoms, too, 
specifying that they are, in turn, connected to S in some way.  The above error 
suggests that x2top is finding a carbon atom that you have not defined in the 
.n2t file.


-Justin






In my case, maybe it considers that 0.18 nm is too much for two atoms
to be connected?


The length defined in the .n2t file should be the actual bond length (from
the coordinate file) +/- 10%, like specbond.dat, if I recall; x2top should
not arbitrarily try to dictate that a bond is too long.

-Justin


-- Forwarded message --
From: Vitaly V. Chaban 
Date: Fri, Feb 5, 2010 at 7:56 PM
Subject: Re: [gmx-users] Re: x2top and bonds. No forcefield type for
atom S (2) with 3 bonds
To: jalem...@vt.edu, gmx-users@gromacs.org


Yes. This worked even with my N2T. I will probably recreate my PDB...


On Fri, Feb 5, 2010 at 7:51 PM, Justin A. Lemkul  wrote:

Vitaly V. Chaban wrote:

Justin,

Am I correct that X2TOP uses only N2T file to make a topology?


Yes.


I made the full line for Sulphur but it didn't change the situation.
It looks strange that X2TOP notices 3 bonds although I propose to have
4 bonds (and they are present). If I propose 3 bonds, it readily gives
an output... This is like it has predefined Sulphur with 3 bonds.


Certainly not.  Take, for example, a simple SO4 molecule:

REMARK
HETATM1  OAC DRG 1   5.850  14.800 -12.770  1.00 20.00
 O
HETATM2  SAE DRG 1   4.810  15.780 -12.710  1.00 20.00
 S
HETATM3  OAD DRG 1   3.550  15.150 -12.980  1.00 20.00
 O
HETATM4  OAB DRG 1   4.770  16.390 -11.340  1.00 20.00
 O
HETATM5  OAA DRG 1   5.070  16.850 -13.730  1.00 20.00
 O

The topology is generated just fine with this .n2t file:

S   S   0   32.06   4   O  0.145O   0.145   O   0.145   O   0.145
O   OM  0   15.9994 1   S  0.145

I don't know what might be going on with your system, but I would suggest
creating an .n2t file with only entries pertinent to your system, for all
atoms involved.  This is, of course, only really useful for debugging,
since
in theory, x2top should be easily extensible by appending the .n2t file.

-Justin


Vitaly


On Fri, Feb 5, 2010 at 7:18 PM, Vitaly V. Chaban 
wrote:

Hi,

This can be the reason when X2TOP gives the following error:
"
Fatal error:
No forcefield type for atom S (2) with 3 bonds
"
?

I try to translate PDB of the TFSA anion
OO
|| ||
F3C-S-N-S-CF3
|| ||
OO

into topology.


My PDB contains optimized geometry:
HEADERTFSA
COMPNDTFSA
AUTHORVVC
ATOM  1  N   TFS 1  -0.000   0.444  -0.008  1.00  0.00
ATOM  2  S   TFS 1   1.401  -0.440  -0.189  1.00  0.00
ATOM  3  S   TFS 1  -1.400  -0.438   0.189  1.00  0.00
ATOM  4  O   TFS 1  -1.236  -1.810  -0.833  1.00  0.00
ATOM  5  O   TFS 1  -1.284  -1.009   1.805  1.00  0.00
ATOM  6  O   TFS 1   1.293  -1.026  -1.800  1.00  0.00
ATOM  7  O   TFS 1   1.233  -1.803   0.845  1.00  0.00
ATOM  8  C   TFS 1  -2.837   0.628  -0.107  1.00  0.00
ATOM  9  C   TFS 1   2.836   0.630   0.105  1.00  0.00
ATOM 10  F   TFS 1  -3.996  -0.097   0.093  1.00  0.00
ATOM 11  F   TFS 1  -2.805   1.094  -1.408  1.00  0.00
ATOM 12  F   TFS 1  -2.807   1.698   0.766  1.00  0.00
ATOM 13  F   TFS 1   2.802   1.099   1.404  1.00  0.00
ATOM 14  F   TFS 1   2.803   1.698  -0.771  1.00  0.00
ATOM 15  F   TFS 1   3.996  -0.093  -0.093  1.00  0.00
END

and my n2t file is

C   C   1   C   ; CNT Carbon with one bond
C   C   2   C   C   : CNT double bonded Carbon
O   O   1   C   ; CARBONYL OXYGEN (C=O)
O   OM  1   C   ; CARBOXYL OXYGEN (CO-)
O   OA  2   C   H   ; HYDROXYL OXYGEN (OH)
O   OW  2   H   H   ; WATER OXYGEN
N   N   3   H   C   C   ; PEPTIDE NITROGEN (N OR NH)
N   NT  3   H   H   C   ; TERMINAL NITROGEN (NH2)
N   NL  4   C   H   H   H

Re: Fwd: [gmx-users] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds

[Vitaly V. Chaban]

On Fri, Feb 5, 2010 at 9:13 PM, Justin A. Lemkul  wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> In this context, it is interesting how X2TOP decides that two atoms
>> are connected? Only on the base of N2T: if the atom should have 4
>> neighbours, it looks for the appropriate number of them?
>>
>
> That's correct.


Then the interesting error is:
"Fatal error:
No forcefield type for atom C (1) with 0 bonds"

while PDB contains other atoms than carbon. If it looks for neighbours
why does not it find them...




>> In my case, maybe it considers that 0.18 nm is too much for two atoms
>> to be connected?
>>
>
> The length defined in the .n2t file should be the actual bond length (from
> the coordinate file) +/- 10%, like specbond.dat, if I recall; x2top should
> not arbitrarily try to dictate that a bond is too long.
>
> -Justin
>
>>
>> -- Forwarded message --
>> From: Vitaly V. Chaban 
>> Date: Fri, Feb 5, 2010 at 7:56 PM
>> Subject: Re: [gmx-users] Re: x2top and bonds. No forcefield type for
>> atom S (2) with 3 bonds
>> To: jalem...@vt.edu, gmx-users@gromacs.org
>>
>>
>> Yes. This worked even with my N2T. I will probably recreate my PDB...
>>
>>
>> On Fri, Feb 5, 2010 at 7:51 PM, Justin A. Lemkul  wrote:
>>>
>>> Vitaly V. Chaban wrote:

 Justin,

 Am I correct that X2TOP uses only N2T file to make a topology?

>>> Yes.
>>>
 I made the full line for Sulphur but it didn't change the situation.
 It looks strange that X2TOP notices 3 bonds although I propose to have
 4 bonds (and they are present). If I propose 3 bonds, it readily gives
 an output... This is like it has predefined Sulphur with 3 bonds.

>>> Certainly not.  Take, for example, a simple SO4 molecule:
>>>
>>> REMARK
>>> HETATM    1  OAC DRG     1       5.850  14.800 -12.770  1.00 20.00
>>>  O
>>> HETATM    2  SAE DRG     1       4.810  15.780 -12.710  1.00 20.00
>>>  S
>>> HETATM    3  OAD DRG     1       3.550  15.150 -12.980  1.00 20.00
>>>  O
>>> HETATM    4  OAB DRG     1       4.770  16.390 -11.340  1.00 20.00
>>>  O
>>> HETATM    5  OAA DRG     1       5.070  16.850 -13.730  1.00 20.00
>>>  O
>>>
>>> The topology is generated just fine with this .n2t file:
>>>
>>> S   S   0   32.06   4   O  0.145    O   0.145   O   0.145   O   0.145
>>> O   OM  0   15.9994 1   S  0.145
>>>
>>> I don't know what might be going on with your system, but I would suggest
>>> creating an .n2t file with only entries pertinent to your system, for all
>>> atoms involved.  This is, of course, only really useful for debugging,
>>> since
>>> in theory, x2top should be easily extensible by appending the .n2t file.
>>>
>>> -Justin
>>>
 Vitaly


 On Fri, Feb 5, 2010 at 7:18 PM, Vitaly V. Chaban 
 wrote:
>
> Hi,
>
> This can be the reason when X2TOP gives the following error:
> "
> Fatal error:
> No forcefield type for atom S (2) with 3 bonds
> "
> ?
>
> I try to translate PDB of the TFSA anion
>     O    O
>     ||     ||
> F3C-S-N-S-CF3
>     ||     ||
>     O    O
>
> into topology.
>
>
> My PDB contains optimized geometry:
> HEADER    TFSA
> COMPND    TFSA
> AUTHOR    VVC
> ATOM      1  N   TFS     1      -0.000   0.444  -0.008  1.00  0.00
> ATOM      2  S   TFS     1       1.401  -0.440  -0.189  1.00  0.00
> ATOM      3  S   TFS     1      -1.400  -0.438   0.189  1.00  0.00
> ATOM      4  O   TFS     1      -1.236  -1.810  -0.833  1.00  0.00
> ATOM      5  O   TFS     1      -1.284  -1.009   1.805  1.00  0.00
> ATOM      6  O   TFS     1       1.293  -1.026  -1.800  1.00  0.00
> ATOM      7  O   TFS     1       1.233  -1.803   0.845  1.00  0.00
> ATOM      8  C   TFS     1      -2.837   0.628  -0.107  1.00  0.00
> ATOM      9  C   TFS     1       2.836   0.630   0.105  1.00  0.00
> ATOM     10  F   TFS     1      -3.996  -0.097   0.093  1.00  0.00
> ATOM     11  F   TFS     1      -2.805   1.094  -1.408  1.00  0.00
> ATOM     12  F   TFS     1      -2.807   1.698   0.766  1.00  0.00
> ATOM     13  F   TFS     1       2.802   1.099   1.404  1.00  0.00
> ATOM     14  F   TFS     1       2.803   1.698  -0.771  1.00  0.00
> ATOM     15  F   TFS     1       3.996  -0.093  -0.093  1.00  0.00
> END
>
> and my n2t file is
>
> C   C   1   C               ; CNT Carbon with one bond
> C   C   2   C   C           : CNT double bonded Carbon
> O   O   1   C               ; CARBONYL OXYGEN (C=O)
> O   OM  1   C               ; CARBOXYL OXYGEN (CO-)
> O   OA  2   C   H           ; HYDROXYL OXYGEN (OH)
> O   OW  2   H   H           ; WATER OXYGEN
> N   N   3   H   C   C       ; PEPTIDE NITROGEN (N OR NH)
> N   NT  3   H   H   C       ; TERMINAL NITROGEN (NH2)
> N   NL  4   C   H   H   H   ; TERMINAL NITROGEN (NH3)
> N   NR5 2   C   C           ; AROMATIC N (5-RING,2 BONDS)
> N   NR5*    3   C   C   H  

Re: [gmx-users] ATP for

[TJ Piggot]

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


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


Cheers

Tom

--On Saturday, February 06, 2010 00:05:10 +0530 Chandan Choudhury 
 wrote:




Hi Thomas !

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


Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA



On Fri, Feb 5, 2010 at 6:54 PM, Thomas Piggot 
wrote:

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

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

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

Cheers

Tom

Chandan Choudhury wrote:


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


Any suggestion will be very helpful.

Chandan


--
Chandan kumar Choudhury
NCL, Pune
INDIA



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

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Re: Fwd: [gmx-users] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds

[Justin A. Lemkul]

Vitaly V. Chaban wrote:

In this context, it is interesting how X2TOP decides that two atoms
are connected? Only on the base of N2T: if the atom should have 4
neighbours, it looks for the appropriate number of them?



That's correct.


In my case, maybe it considers that 0.18 nm is too much for two atoms
to be connected?



The length defined in the .n2t file should be the actual bond length (from the 
coordinate file) +/- 10%, like specbond.dat, if I recall; x2top should not 
arbitrarily try to dictate that a bond is too long.


-Justin



-- Forwarded message --
From: Vitaly V. Chaban 
Date: Fri, Feb 5, 2010 at 7:56 PM
Subject: Re: [gmx-users] Re: x2top and bonds. No forcefield type for
atom S (2) with 3 bonds
To: jalem...@vt.edu, gmx-users@gromacs.org


Yes. This worked even with my N2T. I will probably recreate my PDB...


On Fri, Feb 5, 2010 at 7:51 PM, Justin A. Lemkul  wrote:


Vitaly V. Chaban wrote:

Justin,

Am I correct that X2TOP uses only N2T file to make a topology?


Yes.


I made the full line for Sulphur but it didn't change the situation.
It looks strange that X2TOP notices 3 bonds although I propose to have
4 bonds (and they are present). If I propose 3 bonds, it readily gives
an output... This is like it has predefined Sulphur with 3 bonds.


Certainly not.  Take, for example, a simple SO4 molecule:

REMARK
HETATM1  OAC DRG 1   5.850  14.800 -12.770  1.00 20.00
  O
HETATM2  SAE DRG 1   4.810  15.780 -12.710  1.00 20.00
  S
HETATM3  OAD DRG 1   3.550  15.150 -12.980  1.00 20.00
  O
HETATM4  OAB DRG 1   4.770  16.390 -11.340  1.00 20.00
  O
HETATM5  OAA DRG 1   5.070  16.850 -13.730  1.00 20.00
  O

The topology is generated just fine with this .n2t file:

S   S   0   32.06   4   O  0.145O   0.145   O   0.145   O   0.145
O   OM  0   15.9994 1   S  0.145

I don't know what might be going on with your system, but I would suggest
creating an .n2t file with only entries pertinent to your system, for all
atoms involved.  This is, of course, only really useful for debugging, since
in theory, x2top should be easily extensible by appending the .n2t file.

-Justin


Vitaly


On Fri, Feb 5, 2010 at 7:18 PM, Vitaly V. Chaban 
wrote:

Hi,

This can be the reason when X2TOP gives the following error:
"
Fatal error:
No forcefield type for atom S (2) with 3 bonds
"
?

I try to translate PDB of the TFSA anion
 OO
 || ||
F3C-S-N-S-CF3
 || ||
 OO

into topology.


My PDB contains optimized geometry:
HEADERTFSA
COMPNDTFSA
AUTHORVVC
ATOM  1  N   TFS 1  -0.000   0.444  -0.008  1.00  0.00
ATOM  2  S   TFS 1   1.401  -0.440  -0.189  1.00  0.00
ATOM  3  S   TFS 1  -1.400  -0.438   0.189  1.00  0.00
ATOM  4  O   TFS 1  -1.236  -1.810  -0.833  1.00  0.00
ATOM  5  O   TFS 1  -1.284  -1.009   1.805  1.00  0.00
ATOM  6  O   TFS 1   1.293  -1.026  -1.800  1.00  0.00
ATOM  7  O   TFS 1   1.233  -1.803   0.845  1.00  0.00
ATOM  8  C   TFS 1  -2.837   0.628  -0.107  1.00  0.00
ATOM  9  C   TFS 1   2.836   0.630   0.105  1.00  0.00
ATOM 10  F   TFS 1  -3.996  -0.097   0.093  1.00  0.00
ATOM 11  F   TFS 1  -2.805   1.094  -1.408  1.00  0.00
ATOM 12  F   TFS 1  -2.807   1.698   0.766  1.00  0.00
ATOM 13  F   TFS 1   2.802   1.099   1.404  1.00  0.00
ATOM 14  F   TFS 1   2.803   1.698  -0.771  1.00  0.00
ATOM 15  F   TFS 1   3.996  -0.093  -0.093  1.00  0.00
END

and my n2t file is

C   C   1   C   ; CNT Carbon with one bond
C   C   2   C   C   : CNT double bonded Carbon
O   O   1   C   ; CARBONYL OXYGEN (C=O)
O   OM  1   C   ; CARBOXYL OXYGEN (CO-)
O   OA  2   C   H   ; HYDROXYL OXYGEN (OH)
O   OW  2   H   H   ; WATER OXYGEN
N   N   3   H   C   C   ; PEPTIDE NITROGEN (N OR NH)
N   NT  3   H   H   C   ; TERMINAL NITROGEN (NH2)
N   NL  4   C   H   H   H   ; TERMINAL NITROGEN (NH3)
N   NR5 2   C   C   ; AROMATIC N (5-RING,2 BONDS)
N   NR5*3   C   C   H   ; AROMATIC N (5-RING,3 BONDS)
N   NP  3   C   C   FE  ; PORPHYRIN NITROGEN
C   C   3   C   O   *   ; BARE CARBON (PEPTIDE,C=O,C-N)
; Note that order is importante here because of wildcards.
C   C3  4   H   H   H   *   ; ALIPHATIC CH3 GROUP
C   C2  4   H   H   C   *   ; ALIPHATIC CH2 GROUP
C   C1  4   H   C   *   *   ; ALIPHATIC CH GROUP
C   CB  3   C   C   C   ; BARE CARBON (5-,6-RING)
H   H   1   N   ; HYDROGEN BONDED TO NITROGEN
H   HO  1   O   ; HYDROXYL HYDROGEN
H   HW  1   OW  ; WATER HYDROGEN
H   HS  1   S   ; HYDROGEN BONDED TO SULFUR
H   HC  1   C   ; HYDROGEN BONDED TO CARBON
S   S   4   C  0.181  N  0.167 O 0.172  O  0.172
F   F   1   C



The Sulphur atoms have each 4 bon

Re: [gmx-users] Lennard-Jones Rdf plot

[Justin A. Lemkul]

Lum Nforbi wrote:

Dear all,

   Please, could someone tell me what could be the problem with the 
attached LJ plot?

Could it be due to wrong assignment of periodic boundary conditions?



First, do not attach files without file extensions.  For those of us who are 
security-conscious (some say "paranoid"), we won't open it.  It is much more 
useful to post an image file to some public site, like Photobucket or Google Docs.


Second, there is likely no way anyone can diagnose your problem unless you post 
a very detailed description of what you're doing.  You mention an "LJ plot" but 
the file name of your attachment would suggest a radial distribution function. 
What is it that you are trying to analyze?  How did you produce the plot?  Is it 
indeed an RDF?  If so, what was simulated, and for how long?  What were your 
.mdp parameters?  It is very doubtful that PBC alone caused issues, but rather 
your incorrect assignment of, e.g., cutoffs or some other feature.  But we don't 
know any of this yet.


Remember, we can't get inside your head to know what you're doing.  You've got 
to make it easy for us.


-Justin


Thank you,
Lum



--


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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Fwd: [gmx-users] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds

[Vitaly V. Chaban]

In this context, it is interesting how X2TOP decides that two atoms
are connected? Only on the base of N2T: if the atom should have 4
neighbours, it looks for the appropriate number of them?

In my case, maybe it considers that 0.18 nm is too much for two atoms
to be connected?


-- Forwarded message --
From: Vitaly V. Chaban 
Date: Fri, Feb 5, 2010 at 7:56 PM
Subject: Re: [gmx-users] Re: x2top and bonds. No forcefield type for
atom S (2) with 3 bonds
To: jalem...@vt.edu, gmx-users@gromacs.org


Yes. This worked even with my N2T. I will probably recreate my PDB...


On Fri, Feb 5, 2010 at 7:51 PM, Justin A. Lemkul  wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> Justin,
>>
>> Am I correct that X2TOP uses only N2T file to make a topology?
>>
>
> Yes.
>
>> I made the full line for Sulphur but it didn't change the situation.
>> It looks strange that X2TOP notices 3 bonds although I propose to have
>> 4 bonds (and they are present). If I propose 3 bonds, it readily gives
>> an output... This is like it has predefined Sulphur with 3 bonds.
>>
>
> Certainly not.  Take, for example, a simple SO4 molecule:
>
> REMARK
> HETATM    1  OAC DRG     1       5.850  14.800 -12.770  1.00 20.00
>   O
> HETATM    2  SAE DRG     1       4.810  15.780 -12.710  1.00 20.00
>   S
> HETATM    3  OAD DRG     1       3.550  15.150 -12.980  1.00 20.00
>   O
> HETATM    4  OAB DRG     1       4.770  16.390 -11.340  1.00 20.00
>   O
> HETATM    5  OAA DRG     1       5.070  16.850 -13.730  1.00 20.00
>   O
>
> The topology is generated just fine with this .n2t file:
>
> S   S   0   32.06   4   O  0.145    O   0.145   O   0.145   O   0.145
> O   OM  0   15.9994 1   S  0.145
>
> I don't know what might be going on with your system, but I would suggest
> creating an .n2t file with only entries pertinent to your system, for all
> atoms involved.  This is, of course, only really useful for debugging, since
> in theory, x2top should be easily extensible by appending the .n2t file.
>
> -Justin
>
>> Vitaly
>>
>>
>> On Fri, Feb 5, 2010 at 7:18 PM, Vitaly V. Chaban 
>> wrote:
>>>
>>> Hi,
>>>
>>> This can be the reason when X2TOP gives the following error:
>>> "
>>> Fatal error:
>>> No forcefield type for atom S (2) with 3 bonds
>>> "
>>> ?
>>>
>>> I try to translate PDB of the TFSA anion
>>>      O    O
>>>      ||     ||
>>> F3C-S-N-S-CF3
>>>      ||     ||
>>>      O    O
>>>
>>> into topology.
>>>
>>>
>>> My PDB contains optimized geometry:
>>> HEADER    TFSA
>>> COMPND    TFSA
>>> AUTHOR    VVC
>>> ATOM      1  N   TFS     1      -0.000   0.444  -0.008  1.00  0.00
>>> ATOM      2  S   TFS     1       1.401  -0.440  -0.189  1.00  0.00
>>> ATOM      3  S   TFS     1      -1.400  -0.438   0.189  1.00  0.00
>>> ATOM      4  O   TFS     1      -1.236  -1.810  -0.833  1.00  0.00
>>> ATOM      5  O   TFS     1      -1.284  -1.009   1.805  1.00  0.00
>>> ATOM      6  O   TFS     1       1.293  -1.026  -1.800  1.00  0.00
>>> ATOM      7  O   TFS     1       1.233  -1.803   0.845  1.00  0.00
>>> ATOM      8  C   TFS     1      -2.837   0.628  -0.107  1.00  0.00
>>> ATOM      9  C   TFS     1       2.836   0.630   0.105  1.00  0.00
>>> ATOM     10  F   TFS     1      -3.996  -0.097   0.093  1.00  0.00
>>> ATOM     11  F   TFS     1      -2.805   1.094  -1.408  1.00  0.00
>>> ATOM     12  F   TFS     1      -2.807   1.698   0.766  1.00  0.00
>>> ATOM     13  F   TFS     1       2.802   1.099   1.404  1.00  0.00
>>> ATOM     14  F   TFS     1       2.803   1.698  -0.771  1.00  0.00
>>> ATOM     15  F   TFS     1       3.996  -0.093  -0.093  1.00  0.00
>>> END
>>>
>>> and my n2t file is
>>>
>>> C   C   1   C               ; CNT Carbon with one bond
>>> C   C   2   C   C           : CNT double bonded Carbon
>>> O   O   1   C               ; CARBONYL OXYGEN (C=O)
>>> O   OM  1   C               ; CARBOXYL OXYGEN (CO-)
>>> O   OA  2   C   H           ; HYDROXYL OXYGEN (OH)
>>> O   OW  2   H   H           ; WATER OXYGEN
>>> N   N   3   H   C   C       ; PEPTIDE NITROGEN (N OR NH)
>>> N   NT  3   H   H   C       ; TERMINAL NITROGEN (NH2)
>>> N   NL  4   C   H   H   H   ; TERMINAL NITROGEN (NH3)
>>> N   NR5 2   C   C           ; AROMATIC N (5-RING,2 BONDS)
>>> N   NR5*    3   C   C   H       ; AROMATIC N (5-RING,3 BONDS)
>>> N   NP  3   C   C   FE      ; PORPHYRIN NITROGEN
>>> C   C       3   C   O   *       ; BARE CARBON (PEPTIDE,C=O,C-N)
>>> ; Note that order is importante here because of wildcards.
>>> C   C3  4   H   H   H   *   ; ALIPHATIC CH3 GROUP
>>> C   C2  4   H   H   C   *   ; ALIPHATIC CH2 GROUP
>>> C   C1      4   H   C   *   *   ; ALIPHATIC CH GROUP
>>> C   CB      3   C   C   C       ; BARE CARBON (5-,6-RING)
>>> H   H       1   N               ; HYDROGEN BONDED TO NITROGEN
>>> H   HO      1   O               ; HYDROXYL HYDROGEN
>>> H   HW      1   OW              ; WATER HYDROGEN
>>> H   HS      1   S               ; HYDROGEN BONDED TO SULFUR
>>> H   HC      1   C               ; HYDROGEN BONDED TO CARBON
>>> S   S       4   C  0.181 

[gmx-users] Lennard-Jones Rdf plot

[Lum Nforbi]

Dear all,

   Please, could someone tell me what could be the problem with the attached
LJ plot?
Could it be due to wrong assignment of periodic boundary conditions?

Thank you,
Lum


RDF_oxyxoy
Description: Binary data
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Re: [gmx-users] ATP for

[Chandan Choudhury]

Hi Thomas !

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

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Fri, Feb 5, 2010 at 6:54 PM, Thomas Piggot wrote:

> Not sure about amb2gmx.pl or acpypi but you can do this by hand. Consult
> the GROMACS manual (Chapter 4) for the equations to convert the parameters
> into GROMACS format.
>
> I would also say that the easiest way would be to create a new entry in the
> .rtp and then also add the appropriate bonded parameters into the bon.itp
> file, making sure to include the bonded parameters for the new O3 atom type.
> Do note that you need to also add this new atom type for the O3 oxygen into
> the .atp file and the non-bonded parameters for the atom type into the
> nb.itp file.
>
> You can also add entries into the .hdb to allow pdb2gmx to add the
> appropriate hydrogens to your ATP if so desired. If not, your input pdb for
> pdb2gmx will need to have these hydrogens already included.
>
> Cheers
>
> Tom
>
> Chandan Choudhury wrote:
>
>> Hello gmx users,
>> I need to use ATP's parameter for amber port in gromacs. The atp.prep and
>> frcmod.phos for ATP can be found at
>> http://www.pharmacy.manchester.ac.uk/bryce/amber. How can I use it in
>> ffamber.
>>   The program amb2gmx.pl  needs amber to be installed,
>> which is not present. Same with ACPYPI.
>>
>>
>> Any suggestion will be very helpful.
>>
>> Chandan
>>
>>
>> --
>> Chandan kumar Choudhury
>> NCL, Pune
>> INDIA
>>
>>
> --
> Thomas Piggot
> University of Bristol, UK.
> --
> 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] Topology file for phosphothreonine (TPO) for OPLS force field

[Justin A. Lemkul]

Antoine Delmotte wrote:

Dear gmx-users,

I would like to simulate the CDK9 protein (3BLH in PDB), but there is 
one residue (TPO, phosphothreonine), which Gromacs does not recognise.


I found the PRODRG website as well as force field parameters for TPO for 
the Gromos96.1 force field. However, I would like to use the OPLS-AA 
force field. I therefore need a topology file for this force field, 
which cannot be provided by PRODRG (only useful for united atoms force 
fields).


Does anyone have an idea about where I could get the phosphothreonine 
itp file for OPLS force field?




Search the literature to see if anyone has published parameters for it.

Otherwise, could someone give me clues or the link to a good tutorial 
about how to create this itp file myself?




That's what Chapter 5 of the manual is for, provided you have reliable 
parameters (see below).


Molecular dynamics is something completely new for me so, sorry if I ask 
stupid questions. It also seems I am not the first one to have this 
problem but I could not find any solution on the archive of the mailing 
list.




If MD is completely new to you, and you are unable to find previously published 
and validated parameters, the parameterization of a new species is likely not a 
suitable task.  Parameterization is an expert topic, and it can take many months 
or years to develop reliable parameters, even if you know what you are doing at 
the very start.  Be forewarned:


http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin


I thank you in advance.

Best regards,

Antoine




Hotmail : une messagerie fiable avec la protection anti-spam performante 
de Microsoft Inscrivez-vous 




--


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] Topology file for phosphothreonine (TPO) for OPLS force field

[Antoine Delmotte]

Dear gmx-users,

I would like to simulate the CDK9 protein (3BLH in PDB), but there is one 
residue (TPO, phosphothreonine), which Gromacs does not recognise.

I found the PRODRG website as well as force field parameters for TPO for the 
Gromos96.1 force field. However, I would like to use the OPLS-AA force field. I 
therefore need a topology file for this force field, which cannot be provided 
by PRODRG (only useful for united atoms force fields).

Does anyone have an idea about where I could get the phosphothreonine itp file 
for OPLS force field?

Otherwise, could someone give me clues or the link to a good tutorial about how 
to create this itp file myself? 

Molecular dynamics is something completely new for me so, sorry if I ask stupid 
questions. It also seems I am not the first one to have this problem but I 
could not find any solution on the archive of the mailing list.

I thank you in advance.

Best regards,

Antoine


  
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Re: [gmx-users] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds

[Vitaly V. Chaban]

Yes. This worked even with my N2T. I will probably recreate my PDB...


On Fri, Feb 5, 2010 at 7:51 PM, Justin A. Lemkul  wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> Justin,
>>
>> Am I correct that X2TOP uses only N2T file to make a topology?
>>
>
> Yes.
>
>> I made the full line for Sulphur but it didn't change the situation.
>> It looks strange that X2TOP notices 3 bonds although I propose to have
>> 4 bonds (and they are present). If I propose 3 bonds, it readily gives
>> an output... This is like it has predefined Sulphur with 3 bonds.
>>
>
> Certainly not.  Take, for example, a simple SO4 molecule:
>
> REMARK
> HETATM    1  OAC DRG     1       5.850  14.800 -12.770  1.00 20.00
>   O
> HETATM    2  SAE DRG     1       4.810  15.780 -12.710  1.00 20.00
>   S
> HETATM    3  OAD DRG     1       3.550  15.150 -12.980  1.00 20.00
>   O
> HETATM    4  OAB DRG     1       4.770  16.390 -11.340  1.00 20.00
>   O
> HETATM    5  OAA DRG     1       5.070  16.850 -13.730  1.00 20.00
>   O
>
> The topology is generated just fine with this .n2t file:
>
> S   S   0   32.06   4   O  0.145    O   0.145   O   0.145   O   0.145
> O   OM  0   15.9994 1   S  0.145
>
> I don't know what might be going on with your system, but I would suggest
> creating an .n2t file with only entries pertinent to your system, for all
> atoms involved.  This is, of course, only really useful for debugging, since
> in theory, x2top should be easily extensible by appending the .n2t file.
>
> -Justin
>
>> Vitaly
>>
>>
>> On Fri, Feb 5, 2010 at 7:18 PM, Vitaly V. Chaban 
>> wrote:
>>>
>>> Hi,
>>>
>>> This can be the reason when X2TOP gives the following error:
>>> "
>>> Fatal error:
>>> No forcefield type for atom S (2) with 3 bonds
>>> "
>>> ?
>>>
>>> I try to translate PDB of the TFSA anion
>>>      O    O
>>>      ||     ||
>>> F3C-S-N-S-CF3
>>>      ||     ||
>>>      O    O
>>>
>>> into topology.
>>>
>>>
>>> My PDB contains optimized geometry:
>>> HEADER    TFSA
>>> COMPND    TFSA
>>> AUTHOR    VVC
>>> ATOM      1  N   TFS     1      -0.000   0.444  -0.008  1.00  0.00
>>> ATOM      2  S   TFS     1       1.401  -0.440  -0.189  1.00  0.00
>>> ATOM      3  S   TFS     1      -1.400  -0.438   0.189  1.00  0.00
>>> ATOM      4  O   TFS     1      -1.236  -1.810  -0.833  1.00  0.00
>>> ATOM      5  O   TFS     1      -1.284  -1.009   1.805  1.00  0.00
>>> ATOM      6  O   TFS     1       1.293  -1.026  -1.800  1.00  0.00
>>> ATOM      7  O   TFS     1       1.233  -1.803   0.845  1.00  0.00
>>> ATOM      8  C   TFS     1      -2.837   0.628  -0.107  1.00  0.00
>>> ATOM      9  C   TFS     1       2.836   0.630   0.105  1.00  0.00
>>> ATOM     10  F   TFS     1      -3.996  -0.097   0.093  1.00  0.00
>>> ATOM     11  F   TFS     1      -2.805   1.094  -1.408  1.00  0.00
>>> ATOM     12  F   TFS     1      -2.807   1.698   0.766  1.00  0.00
>>> ATOM     13  F   TFS     1       2.802   1.099   1.404  1.00  0.00
>>> ATOM     14  F   TFS     1       2.803   1.698  -0.771  1.00  0.00
>>> ATOM     15  F   TFS     1       3.996  -0.093  -0.093  1.00  0.00
>>> END
>>>
>>> and my n2t file is
>>>
>>> C   C   1   C               ; CNT Carbon with one bond
>>> C   C   2   C   C           : CNT double bonded Carbon
>>> O   O   1   C               ; CARBONYL OXYGEN (C=O)
>>> O   OM  1   C               ; CARBOXYL OXYGEN (CO-)
>>> O   OA  2   C   H           ; HYDROXYL OXYGEN (OH)
>>> O   OW  2   H   H           ; WATER OXYGEN
>>> N   N   3   H   C   C       ; PEPTIDE NITROGEN (N OR NH)
>>> N   NT  3   H   H   C       ; TERMINAL NITROGEN (NH2)
>>> N   NL  4   C   H   H   H   ; TERMINAL NITROGEN (NH3)
>>> N   NR5 2   C   C           ; AROMATIC N (5-RING,2 BONDS)
>>> N   NR5*    3   C   C   H       ; AROMATIC N (5-RING,3 BONDS)
>>> N   NP  3   C   C   FE      ; PORPHYRIN NITROGEN
>>> C   C       3   C   O   *       ; BARE CARBON (PEPTIDE,C=O,C-N)
>>> ; Note that order is importante here because of wildcards.
>>> C   C3  4   H   H   H   *   ; ALIPHATIC CH3 GROUP
>>> C   C2  4   H   H   C   *   ; ALIPHATIC CH2 GROUP
>>> C   C1      4   H   C   *   *   ; ALIPHATIC CH GROUP
>>> C   CB      3   C   C   C       ; BARE CARBON (5-,6-RING)
>>> H   H       1   N               ; HYDROGEN BONDED TO NITROGEN
>>> H   HO      1   O               ; HYDROXYL HYDROGEN
>>> H   HW      1   OW              ; WATER HYDROGEN
>>> H   HS      1   S               ; HYDROGEN BONDED TO SULFUR
>>> H   HC      1   C               ; HYDROGEN BONDED TO CARBON
>>> S   S       4   C  0.181  N  0.167 O 0.172  O  0.172
>>> F   F       1   C
>>>
>>>
>>>
>>> The Sulphur atoms have each 4 bonds but X2TOP wants them to have only
>>> 3. If I change the string in the N2T to 3 bonds, the topology is
>>> generated but S-C bond is absent.
>>>
>>> What can be the problem?
>>>
>>> Thanks.
>>> --
>>> Vitaly V. Chaban, Ph.D.
>>> http://www-rmn.univer.kharkov.ua/chaban.html
>>>
>>
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Re: [gmx-users] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds

[Justin A. Lemkul]

Vitaly V. Chaban wrote:

Justin,

Am I correct that X2TOP uses only N2T file to make a topology?



Yes.


I made the full line for Sulphur but it didn't change the situation.
It looks strange that X2TOP notices 3 bonds although I propose to have
4 bonds (and they are present). If I propose 3 bonds, it readily gives
an output... This is like it has predefined Sulphur with 3 bonds.



Certainly not.  Take, for example, a simple SO4 molecule:

REMARK
HETATM1  OAC DRG 1   5.850  14.800 -12.770  1.00 20.00 O
HETATM2  SAE DRG 1   4.810  15.780 -12.710  1.00 20.00 S
HETATM3  OAD DRG 1   3.550  15.150 -12.980  1.00 20.00 O
HETATM4  OAB DRG 1   4.770  16.390 -11.340  1.00 20.00 O
HETATM5  OAA DRG 1   5.070  16.850 -13.730  1.00 20.00 O

The topology is generated just fine with this .n2t file:

S   S   0   32.06   4   O  0.145O   0.145   O   0.145   O   0.145
O   OM  0   15.9994 1   S  0.145

I don't know what might be going on with your system, but I would suggest 
creating an .n2t file with only entries pertinent to your system, for all atoms 
involved.  This is, of course, only really useful for debugging, since in 
theory, x2top should be easily extensible by appending the .n2t file.


-Justin


Vitaly


On Fri, Feb 5, 2010 at 7:18 PM, Vitaly V. Chaban  wrote:

Hi,

This can be the reason when X2TOP gives the following error:
"
Fatal error:
No forcefield type for atom S (2) with 3 bonds
"
?

I try to translate PDB of the TFSA anion
  OO
  || ||
F3C-S-N-S-CF3
  || ||
  OO

into topology.


My PDB contains optimized geometry:
HEADERTFSA
COMPNDTFSA
AUTHORVVC
ATOM  1  N   TFS 1  -0.000   0.444  -0.008  1.00  0.00
ATOM  2  S   TFS 1   1.401  -0.440  -0.189  1.00  0.00
ATOM  3  S   TFS 1  -1.400  -0.438   0.189  1.00  0.00
ATOM  4  O   TFS 1  -1.236  -1.810  -0.833  1.00  0.00
ATOM  5  O   TFS 1  -1.284  -1.009   1.805  1.00  0.00
ATOM  6  O   TFS 1   1.293  -1.026  -1.800  1.00  0.00
ATOM  7  O   TFS 1   1.233  -1.803   0.845  1.00  0.00
ATOM  8  C   TFS 1  -2.837   0.628  -0.107  1.00  0.00
ATOM  9  C   TFS 1   2.836   0.630   0.105  1.00  0.00
ATOM 10  F   TFS 1  -3.996  -0.097   0.093  1.00  0.00
ATOM 11  F   TFS 1  -2.805   1.094  -1.408  1.00  0.00
ATOM 12  F   TFS 1  -2.807   1.698   0.766  1.00  0.00
ATOM 13  F   TFS 1   2.802   1.099   1.404  1.00  0.00
ATOM 14  F   TFS 1   2.803   1.698  -0.771  1.00  0.00
ATOM 15  F   TFS 1   3.996  -0.093  -0.093  1.00  0.00
END

and my n2t file is

C   C   1   C   ; CNT Carbon with one bond
C   C   2   C   C   : CNT double bonded Carbon
O   O   1   C   ; CARBONYL OXYGEN (C=O)
O   OM  1   C   ; CARBOXYL OXYGEN (CO-)
O   OA  2   C   H   ; HYDROXYL OXYGEN (OH)
O   OW  2   H   H   ; WATER OXYGEN
N   N   3   H   C   C   ; PEPTIDE NITROGEN (N OR NH)
N   NT  3   H   H   C   ; TERMINAL NITROGEN (NH2)
N   NL  4   C   H   H   H   ; TERMINAL NITROGEN (NH3)
N   NR5 2   C   C   ; AROMATIC N (5-RING,2 BONDS)
N   NR5*3   C   C   H   ; AROMATIC N (5-RING,3 BONDS)
N   NP  3   C   C   FE  ; PORPHYRIN NITROGEN
C   C   3   C   O   *   ; BARE CARBON (PEPTIDE,C=O,C-N)
; Note that order is importante here because of wildcards.
C   C3  4   H   H   H   *   ; ALIPHATIC CH3 GROUP
C   C2  4   H   H   C   *   ; ALIPHATIC CH2 GROUP
C   C1  4   H   C   *   *   ; ALIPHATIC CH GROUP
C   CB  3   C   C   C   ; BARE CARBON (5-,6-RING)
H   H   1   N   ; HYDROGEN BONDED TO NITROGEN
H   HO  1   O   ; HYDROXYL HYDROGEN
H   HW  1   OW  ; WATER HYDROGEN
H   HS  1   S   ; HYDROGEN BONDED TO SULFUR
H   HC  1   C   ; HYDROGEN BONDED TO CARBON
S   S   4   C  0.181  N  0.167 O 0.172  O  0.172
F   F   1   C



The Sulphur atoms have each 4 bonds but X2TOP wants them to have only
3. If I change the string in the N2T to 3 bonds, the topology is
generated but S-C bond is absent.

What can be the problem?

Thanks.
--
Vitaly V. Chaban, Ph.D.
http://www-rmn.univer.kharkov.ua/chaban.html







--


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] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds

[Vitaly V. Chaban]

Justin,

Am I correct that X2TOP uses only N2T file to make a topology?

I made the full line for Sulphur but it didn't change the situation.
It looks strange that X2TOP notices 3 bonds although I propose to have
4 bonds (and they are present). If I propose 3 bonds, it readily gives
an output... This is like it has predefined Sulphur with 3 bonds.

Vitaly


On Fri, Feb 5, 2010 at 7:18 PM, Vitaly V. Chaban  wrote:
> Hi,
>
> This can be the reason when X2TOP gives the following error:
> "
> Fatal error:
> No forcefield type for atom S (2) with 3 bonds
> "
> ?
>
> I try to translate PDB of the TFSA anion
>       O    O
>       ||     ||
> F3C-S-N-S-CF3
>       ||     ||
>       O    O
>
> into topology.
>
>
> My PDB contains optimized geometry:
> HEADER    TFSA
> COMPND    TFSA
> AUTHOR    VVC
> ATOM      1  N   TFS     1      -0.000   0.444  -0.008  1.00  0.00
> ATOM      2  S   TFS     1       1.401  -0.440  -0.189  1.00  0.00
> ATOM      3  S   TFS     1      -1.400  -0.438   0.189  1.00  0.00
> ATOM      4  O   TFS     1      -1.236  -1.810  -0.833  1.00  0.00
> ATOM      5  O   TFS     1      -1.284  -1.009   1.805  1.00  0.00
> ATOM      6  O   TFS     1       1.293  -1.026  -1.800  1.00  0.00
> ATOM      7  O   TFS     1       1.233  -1.803   0.845  1.00  0.00
> ATOM      8  C   TFS     1      -2.837   0.628  -0.107  1.00  0.00
> ATOM      9  C   TFS     1       2.836   0.630   0.105  1.00  0.00
> ATOM     10  F   TFS     1      -3.996  -0.097   0.093  1.00  0.00
> ATOM     11  F   TFS     1      -2.805   1.094  -1.408  1.00  0.00
> ATOM     12  F   TFS     1      -2.807   1.698   0.766  1.00  0.00
> ATOM     13  F   TFS     1       2.802   1.099   1.404  1.00  0.00
> ATOM     14  F   TFS     1       2.803   1.698  -0.771  1.00  0.00
> ATOM     15  F   TFS     1       3.996  -0.093  -0.093  1.00  0.00
> END
>
> and my n2t file is
>
> C   C   1   C               ; CNT Carbon with one bond
> C   C   2   C   C           : CNT double bonded Carbon
> O   O   1   C               ; CARBONYL OXYGEN (C=O)
> O   OM  1   C               ; CARBOXYL OXYGEN (CO-)
> O   OA  2   C   H           ; HYDROXYL OXYGEN (OH)
> O   OW  2   H   H           ; WATER OXYGEN
> N   N   3   H   C   C       ; PEPTIDE NITROGEN (N OR NH)
> N   NT  3   H   H   C       ; TERMINAL NITROGEN (NH2)
> N   NL  4   C   H   H   H   ; TERMINAL NITROGEN (NH3)
> N   NR5 2   C   C           ; AROMATIC N (5-RING,2 BONDS)
> N   NR5*    3   C   C   H       ; AROMATIC N (5-RING,3 BONDS)
> N   NP  3   C   C   FE      ; PORPHYRIN NITROGEN
> C   C       3   C   O   *       ; BARE CARBON (PEPTIDE,C=O,C-N)
> ; Note that order is importante here because of wildcards.
> C   C3  4   H   H   H   *   ; ALIPHATIC CH3 GROUP
> C   C2  4   H   H   C   *   ; ALIPHATIC CH2 GROUP
> C   C1      4   H   C   *   *   ; ALIPHATIC CH GROUP
> C   CB      3   C   C   C       ; BARE CARBON (5-,6-RING)
> H   H       1   N               ; HYDROGEN BONDED TO NITROGEN
> H   HO      1   O               ; HYDROXYL HYDROGEN
> H   HW      1   OW              ; WATER HYDROGEN
> H   HS      1   S               ; HYDROGEN BONDED TO SULFUR
> H   HC      1   C               ; HYDROGEN BONDED TO CARBON
> S   S       4   C  0.181  N  0.167 O 0.172  O  0.172
> F   F       1   C
>
>
>
> The Sulphur atoms have each 4 bonds but X2TOP wants them to have only
> 3. If I change the string in the N2T to 3 bonds, the topology is
> generated but S-C bond is absent.
>
> What can be the problem?
>
> Thanks.
> --
> Vitaly V. Chaban, Ph.D.
> http://www-rmn.univer.kharkov.ua/chaban.html
>



-- 
Vitaly V. Chaban, Ph.D.
http://www-rmn.univer.kharkov.ua/chaban.html
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Re: [gmx-users] problems with intel I7 (2.67 GHz)

[Martti Louhivuori]

[Alexey Shvetsov, 18.12.2009]:
>On Пятница 18 декабря 2009 23:47:34 David van der Spoel wrote:
>>Alexey Shvetsov wrote:
>>>On Пятница 18 декабря 2009 19:29:15 XAvier Periole wrote:
Dears,

we have been trying to run gmx-4.0.X on new machines with the
Intel I7 CPUs. It is a quad core intel on which multi-threading is
a "default" feature. This makes the system to behave as a 8 cores
machine.

We observed some strange behavior of gromacs. Note that is
certainly not due to gromacs itself.

Running jobs using 4 cores we have observed the following behavior:
- the info on the output files (log, xtc, edr ...) is not always printed
- gromacs switches cores, eg: cores 1,2,4,5, and then 2,3,5,6 ... and 
this with no apparent logic.

Jobs using 8 cores become extremely slow, more than expected,
and if running at all.

Running 2 jobs with 4 cores each, one was running with 4 cores, the
second was using only 2 cores although mpirun was asked to use 4.

This is more disturbing since it was also possible to run two jobs
using 4 cores each successfully and have effectively increased
efficiency: each job running at 5/6 of the speed of one run on 4 cores
and running alone.

This was observed with:
- Ubuntu-9.10 (karmic) / kernel linux 2.6.31-14-generic (GNOME 2.28.1)
- openmpi-1.3.2/1.4.X
- gromacs 4.0.5/4.0.7

Anyone has any idea what could be going on on those I7?

Thanks,
We: Djurre (& XAvier)
>>>
>>>Well its usual behavior of systems with HT (Hyper threading) enabled. so
>>>its better to disable HT on such cpus so any cpu eating application like
>>>gromacs will run faster on it.
>>
>>No, this is not what I have heard from Berk Hess, he said that running 8
>>processes on 4 cores gives a speed up of 6-7 times a single core.
>>
>>It sounds more like you need to tune the kernel such that jobs stay on
>>the core they are on. As far as I know Ubuntu is a Desktop OS, maybe you
>>want a Server OS?
>>
>In this case seems cpuaffinity was turned off for mpi apps. check that 
>kernel has cpusets support
>ale...@xeon /misc/_Work/RecA/pca $ zgrep CPUSET /proc/config.gz
>CONFIG_CPUSETS=y
>CONFIG_PROC_PID_CPUSET=y
>
>And check that your openmpi compiled with support of cpusets

The problem of Gromacs stalling on i7 when using multiple CPUs is a MPI
problem. It is most likely caused by a shared memory bug in Open MPI
that was fixed in the latest release (1.4.1).

Switching to openmpi-1.4.1 solves the problem.

Best regards,
-martti-
--
Post-doctoral research fellow
Moleculaire Dynamica | University of Groningen
Nijenborgh 4, 9747AG Groningen, the Netherlands
tel. +(31) 50 363 4339 | fax. +(31) 50 363 4398
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Re: [gmx-users] x2top and bonds. No forcefield type for atom S (2) with 3 bonds

[Justin A. Lemkul]

Vitaly V. Chaban wrote:

Hi,

This can be the reason when X2TOP gives the following error:
"
Fatal error:
No forcefield type for atom S (2) with 3 bonds
"
?

I try to translate PDB of the TFSA anion
   OO
   || ||
F3C-S-N-S-CF3
   || ||
   OO

into topology.


My PDB contains optimized geometry:
HEADERTFSA
COMPNDTFSA
AUTHORVVC
ATOM  1  N   TFS 1  -0.000   0.444  -0.008  1.00  0.00
ATOM  2  S   TFS 1   1.401  -0.440  -0.189  1.00  0.00
ATOM  3  S   TFS 1  -1.400  -0.438   0.189  1.00  0.00
ATOM  4  O   TFS 1  -1.236  -1.810  -0.833  1.00  0.00
ATOM  5  O   TFS 1  -1.284  -1.009   1.805  1.00  0.00
ATOM  6  O   TFS 1   1.293  -1.026  -1.800  1.00  0.00
ATOM  7  O   TFS 1   1.233  -1.803   0.845  1.00  0.00
ATOM  8  C   TFS 1  -2.837   0.628  -0.107  1.00  0.00
ATOM  9  C   TFS 1   2.836   0.630   0.105  1.00  0.00
ATOM 10  F   TFS 1  -3.996  -0.097   0.093  1.00  0.00
ATOM 11  F   TFS 1  -2.805   1.094  -1.408  1.00  0.00
ATOM 12  F   TFS 1  -2.807   1.698   0.766  1.00  0.00
ATOM 13  F   TFS 1   2.802   1.099   1.404  1.00  0.00
ATOM 14  F   TFS 1   2.803   1.698  -0.771  1.00  0.00
ATOM 15  F   TFS 1   3.996  -0.093  -0.093  1.00  0.00
END

and my n2t file is

C   C   1   C   ; CNT Carbon with one bond
C   C   2   C   C   : CNT double bonded Carbon
O   O   1   C   ; CARBONYL OXYGEN (C=O)
O   OM  1   C   ; CARBOXYL OXYGEN (CO-)
O   OA  2   C   H   ; HYDROXYL OXYGEN (OH)
O   OW  2   H   H   ; WATER OXYGEN
N   N   3   H   C   C   ; PEPTIDE NITROGEN (N OR NH)
N   NT  3   H   H   C   ; TERMINAL NITROGEN (NH2)
N   NL  4   C   H   H   H   ; TERMINAL NITROGEN (NH3)
N   NR5 2   C   C   ; AROMATIC N (5-RING,2 BONDS)
N   NR5*3   C   C   H   ; AROMATIC N (5-RING,3 BONDS)
N   NP  3   C   C   FE  ; PORPHYRIN NITROGEN
C   C   3   C   O   *   ; BARE CARBON (PEPTIDE,C=O,C-N)
; Note that order is importante here because of wildcards.
C   C3  4   H   H   H   *   ; ALIPHATIC CH3 GROUP
C   C2  4   H   H   C   *   ; ALIPHATIC CH2 GROUP
C   C1  4   H   C   *   *   ; ALIPHATIC CH GROUP
C   CB  3   C   C   C   ; BARE CARBON (5-,6-RING)
H   H   1   N   ; HYDROGEN BONDED TO NITROGEN
H   HO  1   O   ; HYDROXYL HYDROGEN
H   HW  1   OW  ; WATER HYDROGEN
H   HS  1   S   ; HYDROGEN BONDED TO SULFUR
H   HC  1   C   ; HYDROGEN BONDED TO CARBON
S   S   4   C  0.181  N  0.167 O 0.172  O  0.172
F   F   1   C



The Sulphur atoms have each 4 bonds but X2TOP wants them to have only
3. If I change the string in the N2T to 3 bonds, the topology is
generated but S-C bond is absent.

What can be the problem?



I would start with a properly-formatted .n2t file:

http://www.gromacs.org/Documentation/File_Formats/.n2t_File

-Justin


Thanks.


--


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] x2top and bonds. No forcefield type for atom S (2) with 3 bonds

[Vitaly V. Chaban]

Hi,

This can be the reason when X2TOP gives the following error:
"
Fatal error:
No forcefield type for atom S (2) with 3 bonds
"
?

I try to translate PDB of the TFSA anion
   OO
   || ||
F3C-S-N-S-CF3
   || ||
   OO

into topology.


My PDB contains optimized geometry:
HEADERTFSA
COMPNDTFSA
AUTHORVVC
ATOM  1  N   TFS 1  -0.000   0.444  -0.008  1.00  0.00
ATOM  2  S   TFS 1   1.401  -0.440  -0.189  1.00  0.00
ATOM  3  S   TFS 1  -1.400  -0.438   0.189  1.00  0.00
ATOM  4  O   TFS 1  -1.236  -1.810  -0.833  1.00  0.00
ATOM  5  O   TFS 1  -1.284  -1.009   1.805  1.00  0.00
ATOM  6  O   TFS 1   1.293  -1.026  -1.800  1.00  0.00
ATOM  7  O   TFS 1   1.233  -1.803   0.845  1.00  0.00
ATOM  8  C   TFS 1  -2.837   0.628  -0.107  1.00  0.00
ATOM  9  C   TFS 1   2.836   0.630   0.105  1.00  0.00
ATOM 10  F   TFS 1  -3.996  -0.097   0.093  1.00  0.00
ATOM 11  F   TFS 1  -2.805   1.094  -1.408  1.00  0.00
ATOM 12  F   TFS 1  -2.807   1.698   0.766  1.00  0.00
ATOM 13  F   TFS 1   2.802   1.099   1.404  1.00  0.00
ATOM 14  F   TFS 1   2.803   1.698  -0.771  1.00  0.00
ATOM 15  F   TFS 1   3.996  -0.093  -0.093  1.00  0.00
END

and my n2t file is

C   C   1   C   ; CNT Carbon with one bond
C   C   2   C   C   : CNT double bonded Carbon
O   O   1   C   ; CARBONYL OXYGEN (C=O)
O   OM  1   C   ; CARBOXYL OXYGEN (CO-)
O   OA  2   C   H   ; HYDROXYL OXYGEN (OH)
O   OW  2   H   H   ; WATER OXYGEN
N   N   3   H   C   C   ; PEPTIDE NITROGEN (N OR NH)
N   NT  3   H   H   C   ; TERMINAL NITROGEN (NH2)
N   NL  4   C   H   H   H   ; TERMINAL NITROGEN (NH3)
N   NR5 2   C   C   ; AROMATIC N (5-RING,2 BONDS)
N   NR5*3   C   C   H   ; AROMATIC N (5-RING,3 BONDS)
N   NP  3   C   C   FE  ; PORPHYRIN NITROGEN
C   C   3   C   O   *   ; BARE CARBON (PEPTIDE,C=O,C-N)
; Note that order is importante here because of wildcards.
C   C3  4   H   H   H   *   ; ALIPHATIC CH3 GROUP
C   C2  4   H   H   C   *   ; ALIPHATIC CH2 GROUP
C   C1  4   H   C   *   *   ; ALIPHATIC CH GROUP
C   CB  3   C   C   C   ; BARE CARBON (5-,6-RING)
H   H   1   N   ; HYDROGEN BONDED TO NITROGEN
H   HO  1   O   ; HYDROXYL HYDROGEN
H   HW  1   OW  ; WATER HYDROGEN
H   HS  1   S   ; HYDROGEN BONDED TO SULFUR
H   HC  1   C   ; HYDROGEN BONDED TO CARBON
S   S   4   C  0.181  N  0.167 O 0.172  O  0.172
F   F   1   C



The Sulphur atoms have each 4 bonds but X2TOP wants them to have only
3. If I change the string in the N2T to 3 bonds, the topology is
generated but S-C bond is absent.

What can be the problem?

Thanks.
-- 
Vitaly V. Chaban, Ph.D.
http://www-rmn.univer.kharkov.ua/chaban.html
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[gmx-users] Re: [ gromacs harmonic bond constant

[Vitaly V. Chaban]

OK. I found my function type "1" and used k_b in [kJ/mol/nm^2].

Vitaly


On Fri, Feb 5, 2010 at 5:39 PM, Erik Marklund  wrote:
> It depends on the function type. See the table "Intramolecular interaction
> definitions" in chapter 5 of the gromacs manual. There you can se the units
> associated with the different kinds of interactions.
>
> Erik
>
> Vitaly V. Chaban skrev:
>>
>> Hi,
>>
>> In what units does gromacs MD engine treats harmonic bond constants?
>> In the tutorial, there is a hint about fourth-power potential (related
>> to GROMOS-96 FF) which I guess should have a constant in
>> [kJ/mol/nm^4], but not in [kJ/mol/nm^2]. Although it seems by the
>> absolute value that in the existing FFs (.../top/) including GROMOS96
>> they appear in [kJ/mol/nm^2].
>>
>> If the own FF is used, in what units should one type the values of k_b
>> in topology file for GROMPP to understand it correctly? My variant is
>> [kJ/mol/nm^2]. Please let me know if I'm true.
>>
>> Thanks.
>>
>
>
> --
> ---
> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> er...@xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys
>
>



-- 
Vitaly V. Chaban, Ph.D.
http://www-rmn.univer.kharkov.ua/chaban.html
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Re: [gmx-users] gromacs harmonic bond constant

[Erik Marklund]

It depends on the function type. See the table "Intramolecular 
interaction definitions" in chapter 5 of the gromacs manual. There you 
can se the units associated with the different kinds of interactions.


Erik

Vitaly V. Chaban skrev:

Hi,

In what units does gromacs MD engine treats harmonic bond constants?
In the tutorial, there is a hint about fourth-power potential (related
to GROMOS-96 FF) which I guess should have a constant in
[kJ/mol/nm^4], but not in [kJ/mol/nm^2]. Although it seems by the
absolute value that in the existing FFs (.../top/) including GROMOS96
they appear in [kJ/mol/nm^2].

If the own FF is used, in what units should one type the values of k_b
in topology file for GROMPP to understand it correctly? My variant is
[kJ/mol/nm^2]. Please let me know if I'm true.

Thanks.
  



--
---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys

--
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[gmx-users] gromacs harmonic bond constant

[Vitaly V. Chaban]

Hi,

In what units does gromacs MD engine treats harmonic bond constants?
In the tutorial, there is a hint about fourth-power potential (related
to GROMOS-96 FF) which I guess should have a constant in
[kJ/mol/nm^4], but not in [kJ/mol/nm^2]. Although it seems by the
absolute value that in the existing FFs (.../top/) including GROMOS96
they appear in [kJ/mol/nm^2].

If the own FF is used, in what units should one type the values of k_b
in topology file for GROMPP to understand it correctly? My variant is
[kJ/mol/nm^2]. Please let me know if I'm true.

Thanks.
-- 
Vitaly V. Chaban, Ph.D.
http://www-rmn.univer.kharkov.ua/chaban.html
-- 
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Re: [gmx-users] ATP for

[Thomas Piggot]

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


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


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


Cheers

Tom

Chandan Choudhury wrote:

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


Any suggestion will be very helpful.

Chandan


--
Chandan kumar Choudhury
NCL, Pune
INDIA



--
Thomas Piggot
University of Bristol, UK.
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[gmx-users] RE: gmx-users Digest, Vol 70, Issue 31

[intra\sa175950]

Hi Par,

Thank you so much for your explanations, it is very helpful.

Stéphane 



Hi Stephane,

> I am doing some tests with the CHARMM port in GROMACS. Before to start 
> more extensive simulations with this ff
> I have performed a short run of 1000 TIP3-CHARMM water molecules in a 
> cubic during at T=300 K and P=1.015 bar with v-rescale and PR as 
> thermostat and barostat. I have used the VERSION 
> 4.0.99_development_20090927 of GMX.

good to hear that you could reproduce our results.

> 
> Moreover, since I am not a power user of  GROMACS, I don't know how to 
> translate in GROMACS directives the sentence given in JCTC paper " using 
> a short-range cutoff of 1.2 nm, and van der Waals interactions were 
> switched off between 1.0 to 1.2 nm".
This means coulombtype = PME, rcoulomb = 1.2, vdw-type = switch, rvdw-switch
= 1.0, rvdw = 1.2. 

> And by consequence what are the 
> corrects coulomb and vdw parameters for simulations of CHARMM ff ?
This you should be able to figure out from the CHARMM ff papers. According
to the CMAP paper (MacKerell et al. Journal of Computational Chemistry 2004)
they used real-space (short-range) cutoff of their electrostatic
calculations (using PME) of 8.5 E, and the LJ were switched of between 7.5
to 8.5 E and their neighbor lists had a cutoff of 10.5 E. Remember that we
performed the testing (comparing the energy terms) in the paper without
cut-offs.

/Pdr

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End of gmx-users Digest, Vol 70, Issue 31
*


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[gmx-users] Re: CHARMM TIP3-Water with GMX

[Pär Bjelkmar]

Hi Stephane,

> I am doing some tests with the CHARMM port in GROMACS. Before to start 
> more extensive simulations with this ff
> I have performed a short run of 1000 TIP3-CHARMM water molecules in a 
> cubic during at T=300 K and P=1.015 bar with v-rescale and PR as 
> thermostat and barostat. I have used the VERSION 
> 4.0.99_development_20090927 of GMX.

good to hear that you could reproduce our results.

> 
> Moreover, since I am not a power user of  GROMACS, I don't know how to 
> translate in GROMACS directives the sentence given in JCTC paper " using 
> a short-range cutoff of 1.2 nm, and van der Waals interactions were 
> switched off between 1.0 to 1.2 nm".
This means coulombtype = PME, rcoulomb = 1.2, vdw-type = switch, rvdw-switch = 
1.0, rvdw = 1.2. 

> And by consequence what are the 
> corrects coulomb and vdw parameters for simulations of CHARMM ff ?
This you should be able to figure out from the CHARMM ff papers. According to 
the CMAP paper (MacKerell et al. Journal of Computational Chemistry 2004) they 
used real-space (short-range) cutoff of their electrostatic calculations (using 
PME) of 8.5 Å, and the LJ were switched of between 7.5 to 8.5 Å and their 
neighbor lists had a cutoff of 10.5 Å. Remember that we performed the testing 
(comparing the energy terms) in the paper without cut-offs.

/Pär--
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