Re: [gmx-users] Running MD only for selected part of molecule

[vivek sharma]

Hi Justin,
Thanks for your reply...
and apologies for asking you again.

If I want to keep a part of my molecule fix, say part out of 12 angstrom
radius from the ligand and also want to make avoid energy calculation for
the same, (using energy_excl)
Do I need to mention the separate group for that part of molecule, (as I
already did to make that part position restrained), and next how I will
mention those part in .mdp file...
Is it like...
energy_excl   groupname protein/solvent   (if I want to avoid energy
calculation between the group and protein/solvent)
or something else need to be done than that (like during genpr option).

Please explainAs I have no idea to play with such option...

My apologies again, if these small question irritates you...

With Thanks,
Vivek

2008/10/15 Justin A. Lemkul <[EMAIL PROTECTED]>

>
>
> vivek sharma wrote:
>
>>
>> Dear Justin,
>> Thanks for your reply..
>> But I am not getting how and where should I give the option of
>> energy_excl. For freezing a part of molecule ?
>>
>
> In the .mdp file.
>
>  what are the other checks to be done for the same ?
>>
>>
> I don't know what you're asking.
>
> -Justin
>
>  With Thanks,
>> Vivek
>> 2008/10/14 Justin A. Lemkul <[EMAIL PROTECTED] >
>>
>>
>>
>>vivek sharma wrote:
>>
>>
>>
>>2008/10/14 Justin A. Lemkul <[EMAIL PROTECTED]
>> >
>>>>
>>
>>
>>
>>
>>   vivek sharma wrote:
>>
>>   Hi there,
>>
>>   I tried the mdrun by keeping a group of residue position
>>   restrained, and it is working well (verified by comparing
>>RMSD
>>   plot for the same), thanks for your suggestions regarding
>>the same.
>>   But, I have seen that the part of the molecule I kept for
>>PR is
>>   still having some motion, how can I keep that part rigid ?
>>
>>
>>   Position restraints do not necessarily guarantee that atomic
>>   positions stay absolutely fixed.  Instead, there is an energy
>>   penalty for moving them, which could in some cases be overcome.
>>
>>
>>   I am not getting any idea of energy_excl option mentioned
>>above,
>>   please explain.
>>
>>
>>   The freezegrps option can be used to fix atomic positions, but
>> in
>>   this case large forces can be generated within the frozen
>>group.  As
>>   such, you can apply energygrp_excl to exclude energetic terms
>>within
>>   the frozen group.
>>
>>
>>Will it help me in reducing the time taken for the simulation if
>>I'll keep the part of molecule frozen ?
>>
>>
>>I've never used freezegrps for any large set of atoms, so maybe.  If
>>you've got surrounding solvent, though, the nonbonded interactions
>>are still calculated between the frozen group and solvent, unless
>>you turn that off too.  But then it starts getting really
>>unphysical, in my view.
>>
>>-Justin
>>
>>Thanks,
>>~Vivek
>>
>>
>>
>>   -Justin
>>
>>   With Thanks,
>>   Vivek
>>
>>   2008/10/12 Erik Lindahl <[EMAIL PROTECTED]
>>
>>   >
>>
>>
>>   >
>>
>>
>>  Hi,
>>
>>
>>  On Oct 10, 2008, at 12:46 PM, Justin A. Lemkul wrote:
>>
>>
>>  I want to run MD over a part of my molecule ,
>>for few
>>  residues only (not the whole molecule).
>>  Can I do it using GROMACS ?
>>  I searched for the online documentation and
>>mailing list,
>>  but unable to get appropriate information.
>>  If somebody has already tried such things
>>earlier, please
>>  suggest and direct me for appropriate link and
>>address.
>>
>>
>>  Well, if your goal is to keep certain parts fixed
>>and allow
>>  others to move, probably the easiest way to do it
>>is to apply
>>  position restraints to the "fixed" part.
>>
>>
>>  You can also set parts of the system as a freeze
>>group, in which
>>  case you can exclude all nonbonded interactions inside
>>the freeze
>>  group with the energygrp_excl option in your mdp file.
>>
>>  The main advantage of this is of course that you will
>>improve
>>  performance if 99% of your system is frozen (although all
>>  interactions between the fro

[gmx-users] GROMACS on Bluegene

[Mark Abraham]

Hi,

I can see GROMACS 4.0 has inner loops apparently optimized for BlueGene, 
however the distribution is incomplete. At least the files


interaction.h
nb_kernel_w3_bluegene.h
nb_kernel_w3w3_bluegene.h
nb_kernel_w4_bluegene.h
nb_kernel_w4w4_bluegene.h
nb_kernel_gen_bluegene.h

are missing from src/gmxlib/nonbonded/nb_kernel_bluegene in the official 
distribution.


Further, src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_bluegene.h 
contains the contents of file 
src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel_x86_64_sse.h which 
obviously won't work.


Further, GROMACS configure won't work out-of-the-box on this platform 
(see also 
http://www.gromacs.org/pipermail/gmx-users/2008-October/037179.html and 
discussions on this list months back). Since I can see in the source 
code that Mathias Puetz at IBM has done (at least some of) the 
development work here, then I suggest that IBM may like to provide some 
official build instructions. I have my own black magic that makes 
configure work on my machine, and I'm prepared to make that available 
off-list to interested parties, but I don't know how portable it will be 
between Bluegene installations. A better solution should be available if 
one of the GROMACS developers can approach the IBM people for us, please.


Mark
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Re: [gmx-users] transfer pdb to gro

[Justin A. Lemkul]

He, Yang wrote:

Thank you for your suggestion. I just have a doubt about the pdb file . If we 
need to carry on some practical problems with the gromacs,  how can we get the 
pdb.fill  .Just from the online and then make some modification based on the 
practical project or just write it by ourselves ?  what is the use for those 
pdb.file online?



I don't know what you're asking.  What modifications do you want to make?  What 
types of .pdb files are you thinking of using?  If you're worried about 
formatting issues, I've never had any problems with .pdb files from the RCSB.


I just noticed that none of your messages were sent to the gmx-users listserv; 
just privately to me.  Please be sure to include the users' list on all of your 
messages so that others can weigh in if they have ideas as well.


-Justin


Can you tell me that?

Thank you.

Yang

From: Justin A. Lemkul [EMAIL PROTECTED]
Sent: Thursday, October 16, 2008 10:56 AM
To: He, Yang; Gromacs Users' List
Subject: Re: [gmx-users] transfer pdb to gro

He, Yang wrote:

the operating system is unix and the version is about 3.1.1.  I have no idea 
whether this will influence the result.



Version 3.1.1 is very old; upgrade to a newer version and try again.

-Justin


It always shows like this:

Opening library file /usr/share/gromacs/top/aminoacids.dat
Opening library file /usr/share/gromacs/top/atommass.dat
Opening library file /usr/share/gromacs/top/vdwradii.dat
Opening library file /usr/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Warning: Number of atoms in hao.pdb is 0
Read 0 atoms
Volume: 0 nm^3, corresponds to roughly 0 electrons
No velocities found

My created file is : Gromacs Runs One Microsecond At Cannonball Speeds
0
   2.0   2.0   2.0
no atoms included

Thank you

Yang

From: Justin A. Lemkul [EMAIL PROTECTED]
Sent: Thursday, October 16, 2008 10:47 AM
To: He, Yang; Gromacs Users' List
Subject: Re: [gmx-users] transfer pdb to gro

He, Yang wrote:

Hi Justin.

I just followed the pdb file from you but I can still not create the correct 
gro.file. I use this command  editconf -f hao.pdb -o hao.gro  -d 1.0

What is the problem . And I find what you create for the pdb file based on mine 
almost  makes no difference .


I have no idea what the problem is.  What's in the .gro file?

Sometimes tools don't function properly when they haven't been installed
correctly.  What is your operating system?  What version of Gromacs are you
using?  What were the compilers (and versions)?  Did the installation process
report any errors?

-Justin


Thank you for your guidance.

Yang He


From: Justin A. Lemkul [EMAIL PROTECTED]
Sent: Wednesday, October 15, 2008 5:48 PM
To: He, Yang; Gromacs Users' List
Subject: Re: [gmx-users] transfer pdb to gro

He, Yang wrote:

 So you have created the gro.file . I have tried your pdb.file again but it 
still can not create the gro.file. It is really strange. Can you show me the 
gro.file created based on the pdb.file?


The .gro I created was:

Gyas ROwers Mature At Cryogenic Speed
 8
 1DNA Ab1   0.058   0.052   0.000
 1DNA Tb2   0.016   0.234   0.010
 1DNA S13   0.236   0.657   0.120
 1DNA S24   0.236  -0.657  -0.120
 1DNA P15  -0.063   0.890   0.210
 1DNA P26  -0.063  -0.890  -0.210
 1DNA S37  -0.195   0.670  -0.460
 1DNA S48  -0.195  -0.670   0.460
0.0   0.0   0.0

When running editconf (using the .pdb I pasted below), it correctly detects 8 
atoms.

-Justin


Thank you.

Yang He

From: Justin A. Lemkul [EMAIL PROTECTED]
Sent: Wednesday, October 15, 2008 5:27 PM
To: He, Yang; Gromacs Users' List
Subject: Re: [gmx-users] transfer pdb to gro

He, Yang wrote:

Hi Justin,

Thank you for your reply. I have followed the regular forms about pdb file but 
it still shows that :

___> Opening library file /usr/share/gromacs/top/aminoacids.dat

Opening library file /usr/share/gromacs/top/atommass.dat
Opening library file /usr/share/gromacs/top/vdwradii.dat
Opening library file /usr/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Warning: Number of atoms in atom.pdb is 0
WARNING: all CONECT records are ignored
Read 0 atoms
Volume: 0 nm^3, corresponds to roughly 0 electrons
No velocities found


Then you haven't followed the format correctly.

I created the following from your original .pdb file:

ATOM  1  Ab   DNA   0.5750.516 0.051   1.0  0.0
ATOM  2  Tb   DNA   0.1592.344 0.191   1.0  0.0
ATOM  3  S1   DNA   2.3656.568 1.280   1.0  0.0
ATOM  4  S2   DNA   2.365   -6.568-1.280   1.0  0.0
ATOM  5  P1   DNA  -0.6288.896 2.186   1.0  0.0
ATOM  6  P2   DNA   

Re: [gmx-users] transfer pdb to gro

[Justin A. Lemkul]

He, Yang wrote:

the operating system is unix and the version is about 3.1.1.  I have no idea 
whether this will influence the result.



Version 3.1.1 is very old; upgrade to a newer version and try again.

-Justin


It always shows like this:

Opening library file /usr/share/gromacs/top/aminoacids.dat
Opening library file /usr/share/gromacs/top/atommass.dat
Opening library file /usr/share/gromacs/top/vdwradii.dat
Opening library file /usr/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Warning: Number of atoms in hao.pdb is 0
Read 0 atoms
Volume: 0 nm^3, corresponds to roughly 0 electrons
No velocities found

My created file is : Gromacs Runs One Microsecond At Cannonball Speeds
0
   2.0   2.0   2.0
no atoms included

Thank you

Yang

From: Justin A. Lemkul [EMAIL PROTECTED]
Sent: Thursday, October 16, 2008 10:47 AM
To: He, Yang; Gromacs Users' List
Subject: Re: [gmx-users] transfer pdb to gro

He, Yang wrote:

Hi Justin.

I just followed the pdb file from you but I can still not create the correct 
gro.file. I use this command  editconf -f hao.pdb -o hao.gro  -d 1.0

What is the problem . And I find what you create for the pdb file based on mine 
almost  makes no difference .



I have no idea what the problem is.  What's in the .gro file?

Sometimes tools don't function properly when they haven't been installed
correctly.  What is your operating system?  What version of Gromacs are you
using?  What were the compilers (and versions)?  Did the installation process
report any errors?

-Justin


Thank you for your guidance.

Yang He


From: Justin A. Lemkul [EMAIL PROTECTED]
Sent: Wednesday, October 15, 2008 5:48 PM
To: He, Yang; Gromacs Users' List
Subject: Re: [gmx-users] transfer pdb to gro

He, Yang wrote:

 So you have created the gro.file . I have tried your pdb.file again but it 
still can not create the gro.file. It is really strange. Can you show me the 
gro.file created based on the pdb.file?


The .gro I created was:

Gyas ROwers Mature At Cryogenic Speed
 8
 1DNA Ab1   0.058   0.052   0.000
 1DNA Tb2   0.016   0.234   0.010
 1DNA S13   0.236   0.657   0.120
 1DNA S24   0.236  -0.657  -0.120
 1DNA P15  -0.063   0.890   0.210
 1DNA P26  -0.063  -0.890  -0.210
 1DNA S37  -0.195   0.670  -0.460
 1DNA S48  -0.195  -0.670   0.460
0.0   0.0   0.0

When running editconf (using the .pdb I pasted below), it correctly detects 8 
atoms.

-Justin


Thank you.

Yang He

From: Justin A. Lemkul [EMAIL PROTECTED]
Sent: Wednesday, October 15, 2008 5:27 PM
To: He, Yang; Gromacs Users' List
Subject: Re: [gmx-users] transfer pdb to gro

He, Yang wrote:

Hi Justin,

Thank you for your reply. I have followed the regular forms about pdb file but 
it still shows that :

___> Opening library file /usr/share/gromacs/top/aminoacids.dat

Opening library file /usr/share/gromacs/top/atommass.dat
Opening library file /usr/share/gromacs/top/vdwradii.dat
Opening library file /usr/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Warning: Number of atoms in atom.pdb is 0
WARNING: all CONECT records are ignored
Read 0 atoms
Volume: 0 nm^3, corresponds to roughly 0 electrons
No velocities found


Then you haven't followed the format correctly.

I created the following from your original .pdb file:

ATOM  1  Ab   DNA   0.5750.516 0.051   1.0  0.0
ATOM  2  Tb   DNA   0.1592.344 0.191   1.0  0.0
ATOM  3  S1   DNA   2.3656.568 1.280   1.0  0.0
ATOM  4  S2   DNA   2.365   -6.568-1.280   1.0  0.0
ATOM  5  P1   DNA  -0.6288.896 2.186   1.0  0.0
ATOM  6  P2   DNA  -0.628   -8.896-2.186   1.0  0.0
ATOM  7  S3   DNA  -1.9476.704-4.660   1.0  0.0
ATOM  8  S4   DNA  -1.947   -6.704 4.660   1.0  0.0
CONECT  1  3
CONECT  2  4
CONECT  3  1  5
CONECT  4  2  6
CONECT  5  3  7
CONECT  6  4  8
CONECT  7  5
CONECT  8  6
MASTER00000000   80   80
END

It successfully creates a .gro file.

-Justin


So I think it is because that the atom types such as Sugar ,Adenine base are 
not recognized  by the gromacs .Also, what I want to solve is that how to 
define these big atoms .

Do you know how to define these big atoms in order to make the gromacs  
recognize them and creat the correct gro.file

Thank you .

Yang
From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL 
PROTECTED]
Sent: Wednesday, October 15, 2008 4:36 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] transfer pdb to gro

He, Yang wrote:

Hi all users,

When I use the editconf command to transform pdb file to gro file, it shows 
like t

Re: [gmx-users] transfer pdb to gro

[Justin A. Lemkul]

He, Yang wrote:

Hi Justin.

I just followed the pdb file from you but I can still not create the correct 
gro.file. I use this command  editconf -f hao.pdb -o hao.gro  -d 1.0

What is the problem . And I find what you create for the pdb file based on mine 
almost  makes no difference .



I have no idea what the problem is.  What's in the .gro file?

Sometimes tools don't function properly when they haven't been installed 
correctly.  What is your operating system?  What version of Gromacs are you 
using?  What were the compilers (and versions)?  Did the installation process 
report any errors?


-Justin


Thank you for your guidance.

Yang He


From: Justin A. Lemkul [EMAIL PROTECTED]
Sent: Wednesday, October 15, 2008 5:48 PM
To: He, Yang; Gromacs Users' List
Subject: Re: [gmx-users] transfer pdb to gro

He, Yang wrote:

 So you have created the gro.file . I have tried your pdb.file again but it 
still can not create the gro.file. It is really strange. Can you show me the 
gro.file created based on the pdb.file?



The .gro I created was:

Gyas ROwers Mature At Cryogenic Speed
 8
 1DNA Ab1   0.058   0.052   0.000
 1DNA Tb2   0.016   0.234   0.010
 1DNA S13   0.236   0.657   0.120
 1DNA S24   0.236  -0.657  -0.120
 1DNA P15  -0.063   0.890   0.210
 1DNA P26  -0.063  -0.890  -0.210
 1DNA S37  -0.195   0.670  -0.460
 1DNA S48  -0.195  -0.670   0.460
0.0   0.0   0.0

When running editconf (using the .pdb I pasted below), it correctly detects 8 
atoms.

-Justin


Thank you.

Yang He

From: Justin A. Lemkul [EMAIL PROTECTED]
Sent: Wednesday, October 15, 2008 5:27 PM
To: He, Yang; Gromacs Users' List
Subject: Re: [gmx-users] transfer pdb to gro

He, Yang wrote:

Hi Justin,

Thank you for your reply. I have followed the regular forms about pdb file but 
it still shows that :

___> Opening library file /usr/share/gromacs/top/aminoacids.dat

Opening library file /usr/share/gromacs/top/atommass.dat
Opening library file /usr/share/gromacs/top/vdwradii.dat
Opening library file /usr/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Warning: Number of atoms in atom.pdb is 0
WARNING: all CONECT records are ignored
Read 0 atoms
Volume: 0 nm^3, corresponds to roughly 0 electrons
No velocities found


Then you haven't followed the format correctly.

I created the following from your original .pdb file:

ATOM  1  Ab   DNA   0.5750.516 0.051   1.0  0.0
ATOM  2  Tb   DNA   0.1592.344 0.191   1.0  0.0
ATOM  3  S1   DNA   2.3656.568 1.280   1.0  0.0
ATOM  4  S2   DNA   2.365   -6.568-1.280   1.0  0.0
ATOM  5  P1   DNA  -0.6288.896 2.186   1.0  0.0
ATOM  6  P2   DNA  -0.628   -8.896-2.186   1.0  0.0
ATOM  7  S3   DNA  -1.9476.704-4.660   1.0  0.0
ATOM  8  S4   DNA  -1.947   -6.704 4.660   1.0  0.0
CONECT  1  3
CONECT  2  4
CONECT  3  1  5
CONECT  4  2  6
CONECT  5  3  7
CONECT  6  4  8
CONECT  7  5
CONECT  8  6
MASTER00000000   80   80
END

It successfully creates a .gro file.

-Justin


So I think it is because that the atom types such as Sugar ,Adenine base are 
not recognized  by the gromacs .Also, what I want to solve is that how to 
define these big atoms .

Do you know how to define these big atoms in order to make the gromacs  
recognize them and creat the correct gro.file

Thank you .

Yang
From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL 
PROTECTED]
Sent: Wednesday, October 15, 2008 4:36 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] transfer pdb to gro

He, Yang wrote:

Hi all users,

When I use the editconf command to transform pdb file to gro file, it shows 
like this

Opening library file /usr/share/gromacs/top/aminoacids.dat
Opening library file /usr/share/gromacs/top/atommass.dat
Opening library file /usr/share/gromacs/top/vdwradii.dat
Opening library file /usr/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Warning: Number of atoms in atom.pdb is 0
WARNING: all CONECT records are ignored
Read 0 atoms
Volume: 0 nm^3, corresponds to roughly 0 electrons
No velocities found

And this is my original pdb file

 ATOM   1  Ab   DNA   0.5750.516 0.051   1.0  0.0
 ATOM   2  Tb   DNA   0.1592.344 0.191   1.0  0.0
 ATOM   3  S1   DNA   2.3656.568 1.280   1.0  0.0
 ATOM   4  S2   DNA   2.365   -6.568-1.280   1.0  0.0
 ATOM   5  P1   DNA   -0.628   8.896 2.186   1.0  0.0
 ATOM   6  P2   DNA   -0.628  -8.896-2.186   1.0  0.0
 ATOM   7  S3   DNA  -1.9476.704-4.660   1.0  0.0
 ATOM   8  S4   DNA  -1.947   -6.704  

[gmx-users] Topology file for fullerene c60

[Marine Bozdaganyan]

Dear users!

I'm trying to make forcefield oplsaa for fullerene. I already have modified
files (see it in the end of the letter), but i have a problem with torsion
parameters - torsion angles are different, but atom type is the same -
alkene. Length and angles were taken as an average. After pdb2gmx i have
normal .gro and .top file (but with wrong parameters for torsions). during
the minimization my system blows.

Could anyone give any clue about my problem? May be somebody already has
right topology file for my fullerene.

Thank you in advance.

_

*ffoplsaa.atp*

 opls_141B 12.01100 ; fullerene

__

*ffoplsaanb.itp*

; name bond_type mass charge ptype sigma epsilon

opls_141B C3 6 12.01100 0.000 A 3.47000e-01 2.76470e-01

__

*ffoplsaa.rtp*

[ FUL ]
 [ atoms ]
  CF1 opls_141B 0.000 1
  CF2 opls_141B 0.000 1
  CF3 opls_141B 0.000 1
  CF4 opls_141B 0.000 1
  CF5 opls_141B 0.000 1
  CF6 opls_141B 0.000 1
  .
  CF60 opls_141B 0.000 1
 [ bonds ]
  CF1 CF2
  CF2 CF3
  CF3 CF9
  CF5 CF6
  CF7 CF18
  CF8 CF20
  CF10 CF14
  CF11 CF24
  CF13 CF26
  CF15 CF28
  CF17 CF30

..
  CF19 CF21
  CF21 CF31
  CF23 CF32
  CF25 CF34
  .



*ffoplsaabon.itp*

[ bondtypes ]
; i j func b0 kb
  C3 C3 1 0.14200 265265.6

[ angletypes ]
; i j k func th0 cth
  C3 C3 C3 1 114.000 488.273 ;

[ dihedraltypes ]
; i j k l func coefficients
  C3 C3 C3 C3 3 -4.96013 6.28646 1.30959 -2.63592 0.0 0.0 ;
fullerene
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Re: [gmx-users] Problem building a new polymer using pdb2gmx....

[Alessandro Casoni]

Alberto Sergio Garay ha scritto:

Dear users

I'm trying to build a polymer with a new building block. I have 
included the new
topology block inside the force field rtp file, which I've choosen for 
my simulation (ffG53a6.rtp).
I've also prepared a gro input file, where the atoms of each residue 
follows the same order as in the rtp file

I also added the new residues names in aminoacids.dat

The problem is: when I run pdb2gmx to obtain the topology of my system 
it gives me the following error:


Fatal error:
Atom H1 in residue VBT 2 not found in rtp entry with 24 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.

But there's no H1 atom in my residues. Is pdb2gmx including some extra 
atoms to complete my molecule?

Could anyone give any clue about my problem?

Tank you in advance.

Sergio

below there's a part of my rtp file
...
[ VBT ]
 [ atoms ]
; name   type   charge   chargegroup
  CC1   CH2 0.0 1
  CC2   CH1 0.12000 2
  CR1 C-0.12000 3
  CR2 C-0.14000 4
  HR2HC 0.14000 4
  CR3 C-0.08000 5
  HR3HC 0.08000 5
  CR4 C-0.05000 6
  CT1   CH2 0.37000 6
  NT1NR-0.32000 6
  CR5 C-0.13000 7
  HR5HC 0.13000 7
  CR6 C-0.17000 8
  HR6HC 0.17000 8
  CT2 C-0.21000 9
  HT1HC 0.21000 9
  CT3 C-0.0900010
  CT4   CH3 0.0900010
  CT5 C 0.5800011
  OT1 O-0.5800011
  NT2NR-0.2200012
  HT2 H 0.2200012
  CT6 C 0.5400013
  OT2 O-0.5400013

part of my *.gro file

2VBTCC1   21   3.221   5.305   1.589
2VBTCC2   22   3.143   5.334   1.460
2VBTCR1   23   3.115   5.221   1.384
2VBTCR2   24   3.196   5.155   1.293
2VBTHR2   25   3.305   5.159   1.298
2VBTCR3   26   3.132   5.074   1.200
2VBTHR3   27   3.198   5.003   1.151
2VBTCR4   28   2.995   5.068   1.175
2VBTCT1   29   2.948   5.023   1.052
2VBTNT1   30   3.028   5.038   0.928
2VBTCR5   31   2.919   5.144   1.263
2VBTHR5   32   2.810   5.142   1.268
2VBTCR6   33   2.977   5.208   1.372
2VBTHR6   34   2.916   5.232   1.459
2VBTCT2   35   3.070   4.916   0.874
2VBTHT1   36   3.009   4.827   0.860
2VBTCT3   37   3.190   4.911   0.804
2VBTCT4   38   3.245   4.779   0.750
2VBTCT5   39   3.264   5.027   0.784
2VBTOT1   40   3.364   5.030   0.712
2VBTNT2   41   3.224   5.150   0.839
2VBTHT2   42   3.293   5.223   0.844
2VBTCT6   43   3.100   5.156   0.903
2VBTOT2   44   3.076   5.266   0.952


Hi Sergio, you can try this:

http://davapc1.bioch.dundee.ac.uk/prodrg/index.html

and read the FAQ section...

Alessandro
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Re: [gmx-users] Problem building a new polymer using pdb2gmx....

[David van der Spoel]

Alberto Sergio Garay wrote:

Dear users

I'm trying to build a polymer with a new building block. I have included 
the new
topology block inside the force field rtp file, which I've choosen for 
my simulation (ffG53a6.rtp).
I've also prepared a gro input file, where the atoms of each residue 
follows the same order as in the rtp file

I also added the new residues names in aminoacids.dat

The problem is: when I run pdb2gmx to obtain the topology of my system 
it gives me the following error:


Fatal error:
Atom H1 in residue VBT 2 not found in rtp entry with 24 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.

But there's no H1 atom in my residues. Is pdb2gmx including some extra 
atoms to complete my molecule?

Could anyone give any clue about my problem?


yes. pdb2gmx thinks your molecule is a protein and want to add Hydrogens 
to the termini. Use the -ter flag and select None.


Tank you in advance.

Sergio

below there's a part of my rtp file
...
[ VBT ]
 [ atoms ]
; name   type   charge   chargegroup
  CC1   CH2 0.0 1
  CC2   CH1 0.12000 2
  CR1 C-0.12000 3
  CR2 C-0.14000 4
  HR2HC 0.14000 4
  CR3 C-0.08000 5
  HR3HC 0.08000 5
  CR4 C-0.05000 6
  CT1   CH2 0.37000 6
  NT1NR-0.32000 6
  CR5 C-0.13000 7
  HR5HC 0.13000 7
  CR6 C-0.17000 8
  HR6HC 0.17000 8
  CT2 C-0.21000 9
  HT1HC 0.21000 9
  CT3 C-0.0900010
  CT4   CH3 0.0900010
  CT5 C 0.5800011
  OT1 O-0.5800011
  NT2NR-0.2200012
  HT2 H 0.2200012
  CT6 C 0.5400013
  OT2 O-0.5400013

part of my *.gro file

2VBTCC1   21   3.221   5.305   1.589
2VBTCC2   22   3.143   5.334   1.460
2VBTCR1   23   3.115   5.221   1.384
2VBTCR2   24   3.196   5.155   1.293
2VBTHR2   25   3.305   5.159   1.298
2VBTCR3   26   3.132   5.074   1.200
2VBTHR3   27   3.198   5.003   1.151
2VBTCR4   28   2.995   5.068   1.175
2VBTCT1   29   2.948   5.023   1.052
2VBTNT1   30   3.028   5.038   0.928
2VBTCR5   31   2.919   5.144   1.263
2VBTHR5   32   2.810   5.142   1.268
2VBTCR6   33   2.977   5.208   1.372
2VBTHR6   34   2.916   5.232   1.459
2VBTCT2   35   3.070   4.916   0.874
2VBTHT1   36   3.009   4.827   0.860
2VBTCT3   37   3.190   4.911   0.804
2VBTCT4   38   3.245   4.779   0.750
2VBTCT5   39   3.264   5.027   0.784
2VBTOT1   40   3.364   5.030   0.712
2VBTNT2   41   3.224   5.150   0.839
2VBTHT2   42   3.293   5.223   0.844
2VBTCT6   43   3.100   5.156   0.903
2VBTOT2   44   3.076   5.266   0.952




--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] Problem building a new polymer using pdb2gmx....

[Alberto Sergio Garay]

Dear users

I'm trying to build a polymer with a new building block. I have  
included the new
topology block inside the force field rtp file, which I've choosen for  
my simulation (ffG53a6.rtp).
I've also prepared a gro input file, where the atoms of each residue  
follows the same order as in the rtp file

I also added the new residues names in aminoacids.dat

The problem is: when I run pdb2gmx to obtain the topology of my system  
it gives me the following error:


Fatal error:
Atom H1 in residue VBT 2 not found in rtp entry with 24 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.

But there's no H1 atom in my residues. Is pdb2gmx including some extra  
atoms to complete my molecule?

Could anyone give any clue about my problem?

Tank you in advance.

Sergio

below there's a part of my rtp file
...
[ VBT ]
 [ atoms ]
; name   type   charge   chargegroup
  CC1   CH2 0.0 1
  CC2   CH1 0.12000 2
  CR1 C-0.12000 3
  CR2 C-0.14000 4
  HR2HC 0.14000 4
  CR3 C-0.08000 5
  HR3HC 0.08000 5
  CR4 C-0.05000 6
  CT1   CH2 0.37000 6
  NT1NR-0.32000 6
  CR5 C-0.13000 7
  HR5HC 0.13000 7
  CR6 C-0.17000 8
  HR6HC 0.17000 8
  CT2 C-0.21000 9
  HT1HC 0.21000 9
  CT3 C-0.0900010
  CT4   CH3 0.0900010
  CT5 C 0.5800011
  OT1 O-0.5800011
  NT2NR-0.2200012
  HT2 H 0.2200012
  CT6 C 0.5400013
  OT2 O-0.5400013

part of my *.gro file

2VBTCC1   21   3.221   5.305   1.589
2VBTCC2   22   3.143   5.334   1.460
2VBTCR1   23   3.115   5.221   1.384
2VBTCR2   24   3.196   5.155   1.293
2VBTHR2   25   3.305   5.159   1.298
2VBTCR3   26   3.132   5.074   1.200
2VBTHR3   27   3.198   5.003   1.151
2VBTCR4   28   2.995   5.068   1.175
2VBTCT1   29   2.948   5.023   1.052
2VBTNT1   30   3.028   5.038   0.928
2VBTCR5   31   2.919   5.144   1.263
2VBTHR5   32   2.810   5.142   1.268
2VBTCR6   33   2.977   5.208   1.372
2VBTHR6   34   2.916   5.232   1.459
2VBTCT2   35   3.070   4.916   0.874
2VBTHT1   36   3.009   4.827   0.860
2VBTCT3   37   3.190   4.911   0.804
2VBTCT4   38   3.245   4.779   0.750
2VBTCT5   39   3.264   5.027   0.784
2VBTOT1   40   3.364   5.030   0.712
2VBTNT2   41   3.224   5.150   0.839
2VBTHT2   42   3.293   5.223   0.844
2VBTCT6   43   3.100   5.156   0.903
2VBTOT2   44   3.076   5.266   0.952

--
Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Argentina
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221





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RE: [gmx-users] Unexplained crashes with Gromacs-4.0

[Berk Hess]

Hi,

That issue in 3.3.1 is completely unrelated to this issue in 4.0.

Was your problem in 3.3.1 with parrinello-rahman coupling?
If so, that problem is probably solved by a bug fix in the PR pressure coupling
I introduced in the 4.0 release.

Berk


> Date: Thu, 16 Oct 2008 14:06:19 +0200
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Unexplained crashes with Gromacs-4.0
> 
> Hi,
> 
> I think I had a similar error in GROMACS 3.3.1 (I posted it in June to 
> the User List 
> http://www.gromacs.org/pipermail/gmx-users/2008-June/034411.html). I 
> also got a not reproducable error for the ci variable.
> 
> I made some test and found out that for my system the error occures with 
> semiisotropic pressure coupling and not with isotropic pressure 
> coupling. Another way to avoid the error with semiisotropic pressure 
> coupling was to change from double to single precision. By the way 
> setting tau_p to 5 fs just shifts the error to a later time step.   May 
> be the mistake has something to do with the pressure coupling?
> 
> Till
> 
> 
> Berk Hess wrote:
> >
> >
> >
> >
> > 
> > > Date: Tue, 14 Oct 2008 07:19:45 -0400
> > > From: [EMAIL PROTECTED]
> > > To: gmx-users@gromacs.org
> > > Subject: Re: [gmx-users] Unexplained crashes with Gromacs-4.0
> > >
> > >
> > >
> > > Berk Hess wrote:
> > > > Hi,
> > > >
> > > > I don't really know what could be the problem here.
> > > >
> > > > 0..180 is (confusingly) not including the end, so 180 is out of range.
> > > >
> > > > The only thing I can think of (except for unknown bugs of coarse),
> > > > is that I corrected the coupling time of the Parrinello-Rahman 
> > barostat
> > > > when going from 4.0 RC4 to the official 4.0 release.
> > > > I guess all your old simulations were with older Gromacs releases.
> > > > So to get the same coupling as before, so would need to multiply 
> > tau_t
> > > > by 16.6.
> > > > I don't know if this would help.
> > >
> > > I did see this same error under RC2, but noticed that you fixed this 
> > bug shortly
> > > after I saw it, and that's what I assumed it was. But now I have 
> > seen it under
> > > the official 4.0 release.
> > >
> > > >
> > > > You did not get pressure coupling warnings before the crash?
> > > >
> > >
> > > There are no messages printed before this error pops up. What's really
> > > confusing is that if I simply try the same .tpr file again, it runs 
> > without a
> > > problem. I know that's not terribly scientific, but it seemed odd to 
> > me that my
> > > systems running for 40+ ns suddenly had a problem.
> > >
> > > Is there any diagnostic information I can provide? This problem 
> > seems like it
> > > would be elusive, since even I can't fully reproduce it.
> > >
> > > -Justin
> >
> > If you run in parallel, the dynamic load balancing can affective 
> > reprodibility.
> > You can turn it off with -dlb no
> >
> > Another source of non-reproducibility is FFTW (with PME).
> > By default FFTW times which of different codes is the fastest and uses 
> > that.
> > Configuring FFTW with SSE makes all codes faster and the differences 
> > smaller,
> > so you can configure Gromacs with --disable-fftw-measure to remove
> > the run time optimization without performance loss.
> > For debugging purposes the new -reprod switch of mdrun will try to turn
> > off all optimizations which might affect reproducibilty.
> >
> > Berk
> >
> >
> > 
> > Express yourself instantly with MSN Messenger! MSN Messenger 
> > 
> > 
> >
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.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 [EMAIL PROTECTED]
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> 
> ___
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> http://www.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] Unexplained crashes with Gromacs-4.0

[Till Rudack]

Hi,

I think I had a similar error in GROMACS 3.3.1 (I posted it in June to 
the User List 
http://www.gromacs.org/pipermail/gmx-users/2008-June/034411.html). I 
also got a not reproducable error for the ci variable.


I made some test and found out that for my system the error occures with 
semiisotropic pressure coupling and not with isotropic pressure 
coupling. Another way to avoid the error with semiisotropic pressure 
coupling was to change from double to single precision. By the way 
setting tau_p to 5 fs just shifts the error to a later time step.   May 
be the mistake has something to do with the pressure coupling?


Till


Berk Hess wrote:






> Date: Tue, 14 Oct 2008 07:19:45 -0400
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Unexplained crashes with Gromacs-4.0
>
>
>
> Berk Hess wrote:
> > Hi,
> >
> > I don't really know what could be the problem here.
> >
> > 0..180 is (confusingly) not including the end, so 180 is out of range.
> >
> > The only thing I can think of (except for unknown bugs of coarse),
> > is that I corrected the coupling time of the Parrinello-Rahman 
barostat

> > when going from 4.0 RC4 to the official 4.0 release.
> > I guess all your old simulations were with older Gromacs releases.
> > So to get the same coupling as before, so would need to multiply 
tau_t

> > by 16.6.
> > I don't know if this would help.
>
> I did see this same error under RC2, but noticed that you fixed this 
bug shortly
> after I saw it, and that's what I assumed it was. But now I have 
seen it under

> the official 4.0 release.
>
> >
> > You did not get pressure coupling warnings before the crash?
> >
>
> There are no messages printed before this error pops up. What's really
> confusing is that if I simply try the same .tpr file again, it runs 
without a
> problem. I know that's not terribly scientific, but it seemed odd to 
me that my

> systems running for 40+ ns suddenly had a problem.
>
> Is there any diagnostic information I can provide? This problem 
seems like it

> would be elusive, since even I can't fully reproduce it.
>
> -Justin

If you run in parallel, the dynamic load balancing can affective 
reprodibility.

You can turn it off with -dlb no

Another source of non-reproducibility is FFTW (with PME).
By default FFTW times which of different codes is the fastest and uses 
that.
Configuring FFTW with SSE makes all codes faster and the differences 
smaller,

so you can configure Gromacs with --disable-fftw-measure to remove
the run time optimization without performance loss.
For debugging purposes the new -reprod switch of mdrun will try to turn
off all optimizations which might affect reproducibilty.

Berk



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RE: [gmx-users] Unexplained crashes with Gromacs-4.0

[Berk Hess]

Hi,

I have no clue what the problem could be.
But now I thought a bit longer, I realized that with domain decomposition
the ci error should never occur, since the domain decomposition
puts the charge groups inside the DD cells, so also inside the ns cells.
This seems to indicate that there is a bug somewhere.

We will need all the information we can get, so please file a bugzilla
and include the details on the machine, compiler,
attach the tpr file, log file and mdrun debug files.

Thanks,

Berk

> Date: Wed, 15 Oct 2008 22:14:28 -0400
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Unexplained crashes with Gromacs-4.0
> 
> 
> 
> Berk Hess wrote:
> 
> > 
> > If you run in parallel, the dynamic load balancing can affective 
> > reprodibility.
> > You can turn it off with -dlb no
> 
> I have a situation now that, without fail, has crashed with the same issues 
> I've 
> described before while using "-dlb auto."  Using "-dlb no" the run does not 
> fail.  The .tpr file has now produced that strange error three times, and I 
> have 
> run mdrun with the "-debug 1" flag.  Would providing these .log files and 
> .xvg 
> files provide any useful information?
> 
> I can also provide the .tpr file in a bugzilla, if that would be useful.
> 
> Please let me know and I will upload whatever files you might need.
> 
> -Justin
> 
> > 
> > Another source of non-reproducibility is FFTW (with PME).
> > By default FFTW times which of different codes is the fastest and uses that.
> > Configuring FFTW with SSE makes all codes faster and the differences 
> > smaller,
> > so you can configure Gromacs with --disable-fftw-measure to remove
> > the run time optimization without performance loss.
> > For debugging purposes the new -reprod switch of mdrun will try to turn
> > off all optimizations which might affect reproducibilty.
> > 
> > Berk
> > 
> > 
> > 
> > Express yourself instantly with MSN Messenger! MSN Messenger 
> > 
> > 
> > 
> > 
> > 
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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> > www interface or send it to [EMAIL PROTECTED]
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> 
> -- 
> 
> 
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
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