Re: [gmx-users] Converting Amber frcmod and mol2 files to Gromacs

[Michael Shirts]

ParmEd (http://parmed.github.io/ParmEd/html/index.html) is an
interesting new tool that can help automate such conversions so they
don't need to be done as manually in the future.

On Wed, Sep 30, 2015 at 1:37 PM, Simon Dürr  wrote:
> Hi,
>
> we had the pleasure to convert the *.mol2 and *.frcmod for the HEME
> and CYP prosthetic groups from the following paper  for use with
> GROMACS:
> Shahrokh, K., Orendt, A., Yost, G. S. and Cheatham, T. E. (2012),
> Quantum mechanically derived AMBER-compatible heme parameters for
> various states of the cytochrome P450 catalytic cycle. J. Comput.
> Chem., 33: 119–133. doi: 10.1002/jcc.21922
>
> As the protocol for doing so is rather lengthy we want to share our
> protocol with you guys.
> If you can spare some time we would be grateful If some of you could
> check our procedure.
> If you find any errors let us know. However so far the trajectories
> look good (angles and bond distances are good).
>
> After further testing of the trajectories we want to release the
> rtp/hdb/itp - files.
> Where would be the best way to upload them?
>
> The Protocol is as follows:
>
>
> #
> ##  Table of Contents##
> #
> Part 1: RTP-file
> Part 2: ffbondend-file
> Part 3: ffnonbonded
> Part 4: residuetypes.dat
> Part 5: specbond.dat
> Part 6: hdb-file
> Part 7: atomtypes.atp
>
> ##
> ##  PART 1 ##
> ##
>
> #  BEGIN RTP-File ###
>
> [ HEME ]
>  [ atoms]
>  NC   ncr   0.00660 1
>C1C   ccr  -0.01920 2
>C4C   ccr  -0.01930 3
>C2C   ccr   0.01140 4
>C3C   ccr  -0.03570 5
>…
> [ bonds ]
> NC   C1C
> NC   C4C
> NCFE
>[…]
> ## END RTP-FILE #
>
> The information to fill this file is found in the HEM.mol2 file.
>
> ## HEM.mol2 ##
> @ATOM
>   1 NC  2.946000   -0.972000   -0.732000 nc 1 HEM  0.0066 
>   2 C1C 4.282000   -0.756000   -0.518000 cc 1 HEM -0.0192 
>   4 C2C 5.025000   -1.989000   -0.70 cc 1 HEM  0.0114 
>   5 C3C 4.097000   -2.957000   -1.046000 cc 1 HEM -0.0357 
>   […]
> @BOND
> 1 1 2 1
> 2 1 3 1
> 3 128 1
> ## END HEM.mol2 #
>
> To convert to Gromacs
> 1. take the uppercase name in column 2 of the mol2 which is the name
> found in the PDB input file and put it in column 1 of the [atoms]
> section of the .rtp
> 2. Add the lowercase identifier for GAFF (column 6 in the mol2 ) to
> the second column of the atoms section.
> 3. As we don't want to overwrite any of the normal definitions from
> AMBER99SB-ILDN with GAFF definitions we use a unique name for the GAFF
> atoms. Here we just added "r" at the end of each atom name.
> 4. Add the column 6 of the mol2 with the charge as third column to the
> atoms section
> 5 Group  the atoms to charge groups in the fourth column of the
> [atoms]-section. We put every atom in a new group.
>
> Look at the bonds section in the mol2:
> The first column is the index of the bond, the second column is the id
> of the first atom of the bond, the third column the id of the second
> atom of the bond. The last is the bond type (single or double bond)
>
> 7.Take the id of the first atom and replace it with the uppercase
> identifier from the  ATOM section of the mol2. Do the same for the id
> of the second atom.
>
> The columns 1,3,4,5,7 and 8 in the ATOM section are not relevant for Gromacs.
>
>
> ##
> ##  PART 2 ##
> ##
>
>
> # BEGIN FFBONDED.ITP #
> [ bondtypes ]
> ; ij  func   b0  kb
>  fer ncr10.2   83680 ; IC6.frcmod
> [..]
> [ angletypes ]
>  ;  ijk  func   th0   cth
>  ncr fer ndr   1 85.521 1104.576 ; IC6.frcmod
> [..]
>  [ dihedraltypes ]
>  ;i  j   k  lfunc  phasekd  pn
>  X   SH  fer X   9 180.037.656002 ; IC6.frcmod
> [..]
> [ dihedraltypes ]
>  X   orr crr orr 4 180.04.60240 2 ; GAFF.dat improper
>
>  END FFBONDED.ITP #
>
> The information for this file can be found in the IC6.frcmod file OR
> in the gaff.dat
>
>  IC6.frcmod #
> BOND
> fe-nc 100.000   2.000
> [..]
> ANGLE
> nc-fe-nd  132.000  85.521 # average angle
> [..]
> DIHEDRAL
> X -SH-fe-X   1 9.000 180.000   2.000
> [..]
> IMPROPER
>
> NONBON
> fe 1.8 0.01 1.0
>  END IC6.frcmod 
>
>  BEGIN GAFF.dat ###
> […]
> X -c -c -X41.200   180.000   2.000
> X -o -c -o  1.1   180. 2. JCC,7,(1986),230
>  END GAFF.dat #
>
> To convert to Gromacs
> 1. Add the bonds section:
>  a) Copy the two names of the atoms of the bond. Rename to new
> identifier and separate by a single space.
>  b) Set func to 1 

Re: [gmx-users] Converting Amber frcmod and mol2 files to Gromacs

[Simon Dürr]

Hi Michael,

thanks for the comment. I did not know the program.
It is however not what I'm looking for.

If you have a PDB that makes use of a residue not defined in your
desired FF (in my case Amber99SB-ILDN) and want to use pdb2gmx you
have no other choice than adding it to the FF by hand.
As I did not find good information about it I made this tutorial.

Cheers,
Simon





2015-09-30 13:54 GMT-04:00 Michael Shirts :
> ParmEd (http://parmed.github.io/ParmEd/html/index.html) is an
> interesting new tool that can help automate such conversions so they
> don't need to be done as manually in the future.
>
> On Wed, Sep 30, 2015 at 1:37 PM, Simon Dürr  
> wrote:
>> Hi,
>>
>> we had the pleasure to convert the *.mol2 and *.frcmod for the HEME
>> and CYP prosthetic groups from the following paper  for use with
>> GROMACS:
>> Shahrokh, K., Orendt, A., Yost, G. S. and Cheatham, T. E. (2012),
>> Quantum mechanically derived AMBER-compatible heme parameters for
>> various states of the cytochrome P450 catalytic cycle. J. Comput.
>> Chem., 33: 119–133. doi: 10.1002/jcc.21922
>>
>> As the protocol for doing so is rather lengthy we want to share our
>> protocol with you guys.
>> If you can spare some time we would be grateful If some of you could
>> check our procedure.
>> If you find any errors let us know. However so far the trajectories
>> look good (angles and bond distances are good).
>>
>> After further testing of the trajectories we want to release the
>> rtp/hdb/itp - files.
>> Where would be the best way to upload them?
>>
>> The Protocol is as follows:
>>
>>
>> #
>> ##  Table of Contents##
>> #
>> Part 1: RTP-file
>> Part 2: ffbondend-file
>> Part 3: ffnonbonded
>> Part 4: residuetypes.dat
>> Part 5: specbond.dat
>> Part 6: hdb-file
>> Part 7: atomtypes.atp
>>
>> ##
>> ##  PART 1 ##
>> ##
>>
>> #  BEGIN RTP-File ###
>>
>> [ HEME ]
>>  [ atoms]
>>  NC   ncr   0.00660 1
>>C1C   ccr  -0.01920 2
>>C4C   ccr  -0.01930 3
>>C2C   ccr   0.01140 4
>>C3C   ccr  -0.03570 5
>>…
>> [ bonds ]
>> NC   C1C
>> NC   C4C
>> NCFE
>>[…]
>> ## END RTP-FILE #
>>
>> The information to fill this file is found in the HEM.mol2 file.
>>
>> ## HEM.mol2 ##
>> @ATOM
>>   1 NC  2.946000   -0.972000   -0.732000 nc 1 HEM  0.0066 
>>   2 C1C 4.282000   -0.756000   -0.518000 cc 1 HEM -0.0192 
>>   4 C2C 5.025000   -1.989000   -0.70 cc 1 HEM  0.0114 
>>   5 C3C 4.097000   -2.957000   -1.046000 cc 1 HEM -0.0357 
>>   […]
>> @BOND
>> 1 1 2 1
>> 2 1 3 1
>> 3 128 1
>> ## END HEM.mol2 #
>>
>> To convert to Gromacs
>> 1. take the uppercase name in column 2 of the mol2 which is the name
>> found in the PDB input file and put it in column 1 of the [atoms]
>> section of the .rtp
>> 2. Add the lowercase identifier for GAFF (column 6 in the mol2 ) to
>> the second column of the atoms section.
>> 3. As we don't want to overwrite any of the normal definitions from
>> AMBER99SB-ILDN with GAFF definitions we use a unique name for the GAFF
>> atoms. Here we just added "r" at the end of each atom name.
>> 4. Add the column 6 of the mol2 with the charge as third column to the
>> atoms section
>> 5 Group  the atoms to charge groups in the fourth column of the
>> [atoms]-section. We put every atom in a new group.
>>
>> Look at the bonds section in the mol2:
>> The first column is the index of the bond, the second column is the id
>> of the first atom of the bond, the third column the id of the second
>> atom of the bond. The last is the bond type (single or double bond)
>>
>> 7.Take the id of the first atom and replace it with the uppercase
>> identifier from the  ATOM section of the mol2. Do the same for the id
>> of the second atom.
>>
>> The columns 1,3,4,5,7 and 8 in the ATOM section are not relevant for Gromacs.
>>
>>
>> ##
>> ##  PART 2 ##
>> ##
>>
>>
>> # BEGIN FFBONDED.ITP #
>> [ bondtypes ]
>> ; ij  func   b0  kb
>>  fer ncr10.2   83680 ; IC6.frcmod
>> [..]
>> [ angletypes ]
>>  ;  ijk  func   th0   cth
>>  ncr fer ndr   1 85.521 1104.576 ; IC6.frcmod
>> [..]
>>  [ dihedraltypes ]
>>  ;i  j   k  lfunc  phasekd  pn
>>  X   SH  fer X   9 180.037.656002 ; IC6.frcmod
>> [..]
>> [ dihedraltypes ]
>>  X   orr crr orr 4 180.04.60240 2 ; GAFF.dat improper
>>
>>  END FFBONDED.ITP #
>>
>> The information for this file can be found in the IC6.frcmod file OR
>> in the gaff.dat
>>
>>  IC6.frcmod #
>> BOND
>> fe-nc 100.000   2.000
>> [..]
>> 

[gmx-users] Converting Amber frcmod and mol2 files to Gromacs

[Simon Dürr]

Hi,

we had the pleasure to convert the *.mol2 and *.frcmod for the HEME
and CYP prosthetic groups from the following paper  for use with
GROMACS:
Shahrokh, K., Orendt, A., Yost, G. S. and Cheatham, T. E. (2012),
Quantum mechanically derived AMBER-compatible heme parameters for
various states of the cytochrome P450 catalytic cycle. J. Comput.
Chem., 33: 119–133. doi: 10.1002/jcc.21922

As the protocol for doing so is rather lengthy we want to share our
protocol with you guys.
If you can spare some time we would be grateful If some of you could
check our procedure.
If you find any errors let us know. However so far the trajectories
look good (angles and bond distances are good).

After further testing of the trajectories we want to release the
rtp/hdb/itp - files.
Where would be the best way to upload them?

The Protocol is as follows:


#
##  Table of Contents##
#
Part 1: RTP-file
Part 2: ffbondend-file
Part 3: ffnonbonded
Part 4: residuetypes.dat
Part 5: specbond.dat
Part 6: hdb-file
Part 7: atomtypes.atp

##
##  PART 1 ##
##

#  BEGIN RTP-File ###

[ HEME ]
 [ atoms]
 NC   ncr   0.00660 1
   C1C   ccr  -0.01920 2
   C4C   ccr  -0.01930 3
   C2C   ccr   0.01140 4
   C3C   ccr  -0.03570 5
   …
[ bonds ]
NC   C1C
NC   C4C
NCFE
   […]
## END RTP-FILE #

The information to fill this file is found in the HEM.mol2 file.

## HEM.mol2 ##
@ATOM
  1 NC  2.946000   -0.972000   -0.732000 nc 1 HEM  0.0066 
  2 C1C 4.282000   -0.756000   -0.518000 cc 1 HEM -0.0192 
  4 C2C 5.025000   -1.989000   -0.70 cc 1 HEM  0.0114 
  5 C3C 4.097000   -2.957000   -1.046000 cc 1 HEM -0.0357 
  […]
@BOND
1 1 2 1
2 1 3 1
3 128 1
## END HEM.mol2 #

To convert to Gromacs
1. take the uppercase name in column 2 of the mol2 which is the name
found in the PDB input file and put it in column 1 of the [atoms]
section of the .rtp
2. Add the lowercase identifier for GAFF (column 6 in the mol2 ) to
the second column of the atoms section.
3. As we don't want to overwrite any of the normal definitions from
AMBER99SB-ILDN with GAFF definitions we use a unique name for the GAFF
atoms. Here we just added "r" at the end of each atom name.
4. Add the column 6 of the mol2 with the charge as third column to the
atoms section
5 Group  the atoms to charge groups in the fourth column of the
[atoms]-section. We put every atom in a new group.

Look at the bonds section in the mol2:
The first column is the index of the bond, the second column is the id
of the first atom of the bond, the third column the id of the second
atom of the bond. The last is the bond type (single or double bond)

7.Take the id of the first atom and replace it with the uppercase
identifier from the  ATOM section of the mol2. Do the same for the id
of the second atom.

The columns 1,3,4,5,7 and 8 in the ATOM section are not relevant for Gromacs.


##
##  PART 2 ##
##


# BEGIN FFBONDED.ITP #
[ bondtypes ]
; ij  func   b0  kb
 fer ncr10.2   83680 ; IC6.frcmod
[..]
[ angletypes ]
 ;  ijk  func   th0   cth
 ncr fer ndr   1 85.521 1104.576 ; IC6.frcmod
[..]
 [ dihedraltypes ]
 ;i  j   k  lfunc  phasekd  pn
 X   SH  fer X   9 180.037.656002 ; IC6.frcmod
[..]
[ dihedraltypes ]
 X   orr crr orr 4 180.04.60240 2 ; GAFF.dat improper

 END FFBONDED.ITP #

The information for this file can be found in the IC6.frcmod file OR
in the gaff.dat

 IC6.frcmod #
BOND
fe-nc 100.000   2.000
[..]
ANGLE
nc-fe-nd  132.000  85.521 # average angle
[..]
DIHEDRAL
X -SH-fe-X   1 9.000 180.000   2.000
[..]
IMPROPER

NONBON
fe 1.8 0.01 1.0
 END IC6.frcmod 

 BEGIN GAFF.dat ###
[…]
X -c -c -X41.200   180.000   2.000
X -o -c -o  1.1   180. 2. JCC,7,(1986),230
 END GAFF.dat #

To convert to Gromacs
1. Add the bonds section:
 a) Copy the two names of the atoms of the bond. Rename to new
identifier and separate by a single space.
 b) Set func to 1 (single bond)
 c) Convert the b0 value from the Amber b0 value(in angstroms) as follows

b0(Gro) = b0(amber) / 10  =  [nm]

 d) Convert the kb value from the Amber kb value as follows:

   kb(Gro) = kb(amber) /10  *2  *4.184   = [joule]

2. Add the Angle section
a) Copy the three names of the atoms of the angle. Rename to new
identifier and separate by a single space.
b) Set func to 1 (single bond)
c) Copy the angle from amber
d) Calculate cth as follows

E(amber) = Emin/2
cth = 

Re: [gmx-users] Free energy in octanol and water

[Gmx QA]

Hi Justin

Thanks, that is a good suggestion, I will try that.
Besides running multiple replicates, is there something else that is
obviously wrong with my method?

Best
/PK




2015-09-29 19:09 GMT+02:00 Justin Lemkul :

>
>
> On 9/29/15 4:51 AM, Gmx QA wrote:
>
>> Hi gmx-users
>>
>> I am trying to calculate the free energy of solvation for a drug-molecule
>> in octanol and water.
>>
>> I am comparing two situations:
>>
>> A: Two systems, one with the drug in water only, and one with the drug in
>> pure octanol.
>>
>> B: drug in water only (same as in A), and then one box where I have added
>> 20% water to my octanol system (since mixtures of octanol and water
>> typically contains some water in the octanol phase).
>>
>> Then I run a series of free energy calculations per Justin's tutorial, 48
>> lambda points in total.
>> For system A I get a Delta-G for pure water of 39.07 kJ/mol, and 92.81
>> kJ/mol in pure octanol.
>>
>> For system B, the Delta-G for pure water is the same, but for the
>> octanol-box with 20% water the Delta-G is 95.99 kJ/mol.
>>
>> All of these results are obtained using gmx bar in gromacs 5.0.4.
>>
>> My main concern is that the Delta-G is higher in the water/octanol mixture
>> than in pure octanol, but I would have expected the reverse to be the
>> case?
>>
>>
> From experience, I can tell you it is very hard to get good convergence on
> such mixtures.  You'll note that in npt.gro you effectively have two bands
> of water formed in the box, neither or which is particularly close to the
> API molecule. You'll probably get some microscopic phase separation.  The
> route I've gone in the past is to generate several starting configurations
> (different random seeds when inserting the water molecules) and averaging
> over multiple runs.  You should also do some error analysis of your results
> (both block averaging for convergence, and to compare the two DG values
> between the systems).  Without error bars, you have no idea if those two
> values are at all meaningfully different.
>
> -Justin
>
> Is there something wrong with my protocol? The forcefield is
>> GAFF/amber99sb,and all production runs are 10 ns in length.
>>
>> Best
>> /PK
>>
>> I have uploaded copies of all input-files here:
>>
>> https://dl.dropboxusercontent.com/u/66785227/md.mdp
>> https://dl.dropboxusercontent.com/u/66785227/npt.gro
>> https://dl.dropboxusercontent.com/u/66785227/octanol_GMX.itp
>> https://dl.dropboxusercontent.com/u/66785227/API_gmx.itp
>> https://dl.dropboxusercontent.com/u/66785227/topol.top
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Teemu Murtola]

Thanks for testing it, I see that there is still room for improvement in
getting more context information into the error messages. I'm a bit
confused by the difference between your original report of system.xtc vs
traj.xtc in the new message, but that may not matter that much. Is your xtc
file larger that 2GB in size?

On Wed, Sep 30, 2015, 07:53 Venkat Reddy  wrote:

> Hi Teemu,
> Thank you for providing the patch. But the patched version is giving
> following error message:
>
> Program: gmx rdf, VERSION 5.2-dev
> Source file: src/gromacs/utility/path.cpp (line 406)
> Function:static void gmx::File::throwOnError(const
> gmx::File::NotFoundInfo&)
>
> System I/O error:
> Failed to access file 'traj.xtc'.
> The file could not be opened.
>   Reason: Value too large for defined data type
>   (call to fopen() returned error code 75)
>
> I would like to inform you that I have installed this patched version to a
> non-standard location.
>
>
> On Wed, Sep 30, 2015 at 8:39 AM, Teemu Murtola 
> wrote:
>
> > Hi,
> >
> > I now changed the check to provide more details (in 5140
> > ). If you haven't figured out what the
> > issue was, you could try building the source code from the above link,
> and
> > running it to get more details.
> >
> > There is not much we can do to help diagnose the issue further, unless
> you
> > can provide additional information on the file system contents. Also note
> > that if you provide an input file name that looks like a valid file name
> > (with the correct extension), Gromacs 5.1 will use it as is, or give an
> > error if it does not exist. Previous versions silently tried to append
> all
> > kinds of extensions if the file did not exist (or could not be read) even
> > in such a case, and could then use some other file as input.
> >
> > Best regards,
> > Teemu
> >
> > On Sat, Sep 26, 2015 at 11:56 AM Teemu Murtola 
> > wrote:
> >
> > > This error has nothing to do with the contents of the file, but rather
> > the
> > > operating system appears to be telling Gromacs that the file cannot be
> > > opened or that it is not a regular file. With the information here,
> it's
> > > difficult to say anything more; if you want to debug this further, the
> > > relevant function is gmx::File::exists().
> > >
> > > It would be useful to know what's the problem so that the check (or the
> > > error message) can be improved.
> > >
> > > Best regards,
> > > Teemu
> > >
> > > On Fri, Sep 25, 2015, 21:20 Venkat Reddy  wrote:
> > >
> > >> Hi Tsjerk,
> > >> Thank you for the quick reply. Yes I can access it with other
> versions,
> > >> like 4.5.5, 5.0.4.
> > >>
> > >> On Fri, Sep 25, 2015 at 11:33 PM, Tsjerk Wassenaar  >
> > >> wrote:
> > >>
> > >> > Hi Venkat,
> > >> >
> > >> > Does it exist? Is it accessible? The XTC format did not change since
> > the
> > >> > early years of Gromacs. Can you access it with a different version?
> > >> >
> > >> > Cheers,
> > >> >
> > >> > Tsjerk
> > >> > On Sep 25, 2015 19:52, "Venkat Reddy"  wrote:
> > >> >
> > >> > > Dear all,
> > >> > > I have a trajectory file generated by gromacs-4.5.5. Recently I
> > tried
> > >> to
> > >> > > plot radial distribution function using 'gmx rdf' tool available
> in
> > >> > > gromacs-5.1. But I am getting the following error.
> > >> > > Error in user input:
> > >> > > Invalid command-line options
> > >> > >   In command-line option -f
> > >> > > File 'system.xtc' does not exist or is not accessible.
> > >> > >
> > >> > > I knew that gromacs old trajectories can be analysed using new
> > version
> > >> > > tools. But why I am facing this error?
> > >> > >
> > >> > >
> > >> > > With regards
> > >> > > Venkat Reddy Chirasani
> > >> > > PhD student
> > >> > > Laboratory of Computational Biophysics
> > >> > > Department of Biotechnology
> > >> > > IIT Madras
> > >> > > Chennai
> > >> > > INDIA-600036
> > >> > > --
> > >> > > Gromacs Users mailing list
> > >> > >
> > >> > > * Please search the archive at
> > >> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> before
> > >> > > posting!
> > >> > >
> > >> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >> > >
> > >> > > * For (un)subscribe requests visit
> > >> > >
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > >> > > send a mail to gmx-users-requ...@gromacs.org.
> > >> > >
> > >> > --
> > >> > Gromacs Users mailing list
> > >> >
> > >> > * Please search the archive at
> > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >> > posting!
> > >> >
> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >> >
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> > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > >> > send a mail to gmx-users-requ...@gromacs.org.
> > >> >
> > 

[gmx-users] Simulations of proteins in membrane bilayer

[??????]

Hi All:

I am doing a simulation in which a protein is inserted into a bilayer. In my 
simulations, the protein moved on the x-y plane of the bilayer (which is 
normal). However, in order to do some analysis, I have to put the protein to 
the center of the box, but still keep the box filled by lipids. Does anyone 
know how to do this?
Of course, I could put the protein to the center of the box by align the 
protein with that in the first snapshot, but in this way, some of the lipids 
will be out of the PBC box. In my case, I have to keep all of the lipids in the 
PBC box and packed around the protein. 

I am really appreciate for your suggestions and help. 

With my best regards, 
RXG
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Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Venkat Reddy]

Hi Teemu,
Thanks for the prompt reply. Yes, the xtc file size is larger than 2GB
(approx. 50GB) and both system.xtc and traj.xtc are same files. I am
extremely sorry for the confusion :)

On Wed, Sep 30, 2015 at 11:31 AM, Teemu Murtola 
wrote:

> Thanks for testing it, I see that there is still room for improvement in
> getting more context information into the error messages. I'm a bit
> confused by the difference between your original report of system.xtc vs
> traj.xtc in the new message, but that may not matter that much. Is your xtc
> file larger that 2GB in size?
>
> On Wed, Sep 30, 2015, 07:53 Venkat Reddy  wrote:
>
> > Hi Teemu,
> > Thank you for providing the patch. But the patched version is giving
> > following error message:
> >
> > Program: gmx rdf, VERSION 5.2-dev
> > Source file: src/gromacs/utility/path.cpp (line 406)
> > Function:static void gmx::File::throwOnError(const
> > gmx::File::NotFoundInfo&)
> >
> > System I/O error:
> > Failed to access file 'traj.xtc'.
> > The file could not be opened.
> >   Reason: Value too large for defined data type
> >   (call to fopen() returned error code 75)
> >
> > I would like to inform you that I have installed this patched version to
> a
> > non-standard location.
> >
> >
> > On Wed, Sep 30, 2015 at 8:39 AM, Teemu Murtola 
> > wrote:
> >
> > > Hi,
> > >
> > > I now changed the check to provide more details (in 5140
> > > ). If you haven't figured out what
> the
> > > issue was, you could try building the source code from the above link,
> > and
> > > running it to get more details.
> > >
> > > There is not much we can do to help diagnose the issue further, unless
> > you
> > > can provide additional information on the file system contents. Also
> note
> > > that if you provide an input file name that looks like a valid file
> name
> > > (with the correct extension), Gromacs 5.1 will use it as is, or give an
> > > error if it does not exist. Previous versions silently tried to append
> > all
> > > kinds of extensions if the file did not exist (or could not be read)
> even
> > > in such a case, and could then use some other file as input.
> > >
> > > Best regards,
> > > Teemu
> > >
> > > On Sat, Sep 26, 2015 at 11:56 AM Teemu Murtola <
> teemu.murt...@gmail.com>
> > > wrote:
> > >
> > > > This error has nothing to do with the contents of the file, but
> rather
> > > the
> > > > operating system appears to be telling Gromacs that the file cannot
> be
> > > > opened or that it is not a regular file. With the information here,
> > it's
> > > > difficult to say anything more; if you want to debug this further,
> the
> > > > relevant function is gmx::File::exists().
> > > >
> > > > It would be useful to know what's the problem so that the check (or
> the
> > > > error message) can be improved.
> > > >
> > > > Best regards,
> > > > Teemu
> > > >
> > > > On Fri, Sep 25, 2015, 21:20 Venkat Reddy 
> wrote:
> > > >
> > > >> Hi Tsjerk,
> > > >> Thank you for the quick reply. Yes I can access it with other
> > versions,
> > > >> like 4.5.5, 5.0.4.
> > > >>
> > > >> On Fri, Sep 25, 2015 at 11:33 PM, Tsjerk Wassenaar <
> tsje...@gmail.com
> > >
> > > >> wrote:
> > > >>
> > > >> > Hi Venkat,
> > > >> >
> > > >> > Does it exist? Is it accessible? The XTC format did not change
> since
> > > the
> > > >> > early years of Gromacs. Can you access it with a different
> version?
> > > >> >
> > > >> > Cheers,
> > > >> >
> > > >> > Tsjerk
> > > >> > On Sep 25, 2015 19:52, "Venkat Reddy" 
> wrote:
> > > >> >
> > > >> > > Dear all,
> > > >> > > I have a trajectory file generated by gromacs-4.5.5. Recently I
> > > tried
> > > >> to
> > > >> > > plot radial distribution function using 'gmx rdf' tool available
> > in
> > > >> > > gromacs-5.1. But I am getting the following error.
> > > >> > > Error in user input:
> > > >> > > Invalid command-line options
> > > >> > >   In command-line option -f
> > > >> > > File 'system.xtc' does not exist or is not accessible.
> > > >> > >
> > > >> > > I knew that gromacs old trajectories can be analysed using new
> > > version
> > > >> > > tools. But why I am facing this error?
> > > >> > >
> > > >> > >
> > > >> > > With regards
> > > >> > > Venkat Reddy Chirasani
> > > >> > > PhD student
> > > >> > > Laboratory of Computational Biophysics
> > > >> > > Department of Biotechnology
> > > >> > > IIT Madras
> > > >> > > Chennai
> > > >> > > INDIA-600036
> > > >> > > --
> > > >> > > Gromacs Users mailing list
> > > >> > >
> > > >> > > * Please search the archive at
> > > >> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> > before
> > > >> > > posting!
> > > >> > >
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> > > >> > >
> > > >> > > * For (un)subscribe requests visit
> > > >> > >
> > 

[gmx-users] mutating the protein

[Raag Saluja]

Hi!

Gromacs is a beautiful software!  I have been able to understand the
dynamics of this protein I was trying to study.

I wanted to see how the various amino acids could affect its dynamics. So I
wanted to mutate the protein by replacing one particular amino acid by
another one. How may I do that?

Thank you in advance!

-- 
Regards,
Raag
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Re: [gmx-users] mutating the protein

[Repic Matej]

I do not think this is something gromacs supports, but you can use several
other programs like VMD, Chimera, Modeler etc, depending on the method of
mutating a residue. I usually use chimera on macosx or linux like this:

echo "open protein.pdb; swapaa leu :333.a; write 0 333leu.pdb" | chimera
--nogui

This command opens the protein.pdb, swaps the amino acid 333 on chain a,
and saves the pdb as 333leu.pdb.

Best,


--
Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC ­ LCBC
BCH 4108
CH - 1015 Lausanne
--







On 9/30/15, 11:55, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Raag Saluja"  wrote:

>Hi!
>
>Gromacs is a beautiful software!  I have been able to understand the
>dynamics of this protein I was trying to study.
>
>I wanted to see how the various amino acids could affect its dynamics. So
>I
>wanted to mutate the protein by replacing one particular amino acid by
>another one. How may I do that?
>
>Thank you in advance!
>
>-- 
>Regards,
>Raag
>-- 
>Gromacs Users mailing list
>
>* Please search the archive at
>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>posting!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>send a mail to gmx-users-requ...@gromacs.org.

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Re: [gmx-users] Gromacs GPU got hang

[Téletchéa Stéphane]

Le 29/09/2015 23:40, M Teguh Satria a écrit :

Any of you experiencing similar problem ? Is there any way to
troubleshoot/debug to see the cause ? Because I didn't get any warning or
error message.


Hello,

This can be a driver issue (or hardware, think of temperature, dust, ...),
and happens to me from time to time.

The only solution I found was to reset the GPU (see nvidia-smi options),
if this is not sufficient you will have to reboot (and use the cold boot:
turn off the computer for more than 30s, and then boot again).

If this happens too often, you may have a defective card, see your 
vendor in that

case...

Best,

Stéphane Téletchéa

--
Assistant Professor, UFIP, UMR 6286 CNRS, Team Protein Design In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes 
cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org

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[gmx-users] bond, angles and dihedrals in the topology file

[faride badalkhani]

Dear all,

Could you tell me what is wrong when there are some strange bond, angles
and dihedrals in the topology file after executing pdb2gmx command?
for example atoms 1 and 27 do not have any connectivity, but pdb2gmx
generate them as [bonds]. A similar problem occurs in case of angles and
dihedrals.

Truly yours,
Farideh
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Re: [gmx-users] mutating the protein

[Catarina A. Carvalheda dos Santos]

Hi there,

I don't know about other options, but PyMOL allows you to do this using the
"Mutagenesis Wizard" (just google it and you'll find step-by-step
instructions in the PyMOL Wiki).
Whatever you use, make sure that you select a proper side chain orientation
(rotamer) when performing the mutation. This will avoid clashes between
protein atoms and therefore problems during the energy minimization step.

Regards,




On 30 September 2015 at 12:19, Repic Matej  wrote:

> I do not think this is something gromacs supports, but you can use several
> other programs like VMD, Chimera, Modeler etc, depending on the method of
> mutating a residue. I usually use chimera on macosx or linux like this:
>
> echo "open protein.pdb; swapaa leu :333.a; write 0 333leu.pdb" | chimera
> --nogui
>
> This command opens the protein.pdb, swaps the amino acid 333 on chain a,
> and saves the pdb as 333leu.pdb.
>
> Best,
>
>
> --
> Dr. Matej Repic
> Ecole Polytechnique Fédérale de Lausanne
> Laboratory of Computational Chemistry and Biochemistry
> SB - ISIC ­ LCBC
> BCH 4108
> CH - 1015 Lausanne
> --
>
>
>
>
>
>
>
> On 9/30/15, 11:55, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
> behalf of Raag Saluja"  on behalf of saluja.r...@gmail.com> wrote:
>
> >Hi!
> >
> >Gromacs is a beautiful software!  I have been able to understand the
> >dynamics of this protein I was trying to study.
> >
> >I wanted to see how the various amino acids could affect its dynamics. So
> >I
> >wanted to mutate the protein by replacing one particular amino acid by
> >another one. How may I do that?
> >
> >Thank you in advance!
> >
> >--
> >Regards,
> >Raag
> >--
> >Gromacs Users mailing list
> >
> >* Please search the archive at
> >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >posting!
> >
> >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >* For (un)subscribe requests visit
> >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >send a mail to gmx-users-requ...@gromacs.org.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
School of Life Sciences
University of Dundee
DD1 5EH, Dundee, Scotland, UK
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Re: [gmx-users] Free energy in octanol and water

[Justin Lemkul]

On 9/30/15 3:13 AM, Gmx QA wrote:

Hi Justin

Thanks, that is a good suggestion, I will try that.
Besides running multiple replicates, is there something else that is
obviously wrong with my method?



Not that I can see.

-Justin


Best
/PK




2015-09-29 19:09 GMT+02:00 Justin Lemkul :




On 9/29/15 4:51 AM, Gmx QA wrote:


Hi gmx-users

I am trying to calculate the free energy of solvation for a drug-molecule
in octanol and water.

I am comparing two situations:

A: Two systems, one with the drug in water only, and one with the drug in
pure octanol.

B: drug in water only (same as in A), and then one box where I have added
20% water to my octanol system (since mixtures of octanol and water
typically contains some water in the octanol phase).

Then I run a series of free energy calculations per Justin's tutorial, 48
lambda points in total.
For system A I get a Delta-G for pure water of 39.07 kJ/mol, and 92.81
kJ/mol in pure octanol.

For system B, the Delta-G for pure water is the same, but for the
octanol-box with 20% water the Delta-G is 95.99 kJ/mol.

All of these results are obtained using gmx bar in gromacs 5.0.4.

My main concern is that the Delta-G is higher in the water/octanol mixture
than in pure octanol, but I would have expected the reverse to be the
case?



 From experience, I can tell you it is very hard to get good convergence on
such mixtures.  You'll note that in npt.gro you effectively have two bands
of water formed in the box, neither or which is particularly close to the
API molecule. You'll probably get some microscopic phase separation.  The
route I've gone in the past is to generate several starting configurations
(different random seeds when inserting the water molecules) and averaging
over multiple runs.  You should also do some error analysis of your results
(both block averaging for convergence, and to compare the two DG values
between the systems).  Without error bars, you have no idea if those two
values are at all meaningfully different.

-Justin

Is there something wrong with my protocol? The forcefield is

GAFF/amber99sb,and all production runs are 10 ns in length.

Best
/PK

I have uploaded copies of all input-files here:

https://dl.dropboxusercontent.com/u/66785227/md.mdp
https://dl.dropboxusercontent.com/u/66785227/npt.gro
https://dl.dropboxusercontent.com/u/66785227/octanol_GMX.itp
https://dl.dropboxusercontent.com/u/66785227/API_gmx.itp
https://dl.dropboxusercontent.com/u/66785227/topol.top



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] bond, angles and dihedrals in the topology file

[Justin Lemkul]

On 9/30/15 7:21 AM, faride badalkhani wrote:

Dear all,

Could you tell me what is wrong when there are some strange bond, angles
and dihedrals in the topology file after executing pdb2gmx command?
for example atoms 1 and 27 do not have any connectivity, but pdb2gmx
generate them as [bonds]. A similar problem occurs in case of angles and
dihedrals.



Impossible to say without knowing what you're actually doing.  Please always 
provide a full description of your system, your pdb2gmx command, and any 
relevant output, snippets of files, etc.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] bond, angles and dihedrals in the topology file

[faride badalkhani]

I want to simulate a dendrimer (a hyperbranched polymer) in water. I have
used the GROMOS 53A6 force field parameters, and I have done the following
steps:
1- Defining new atom types that were not exist in .atp file.
2- Adding appropriate bonds, angles, dihedrals, and impropers into the
ffbonded.itp file.
3- Defining nonbonded parameters in ffnonbonded.itp file according to
GROMOS FF parameters.
4- Introducing residue building blocks along with [bonds], [angles],
[impropers], and [dihedrals] in .rtp file.

After using pdb2gmx I receive this command:

You have successfully generated a topology from: g3n.pdb
The CA force field and the spce water model are used.

Then I define box and solvent without any problems, but there are many
errors when I execute grompp command as follows:
Error 892 [file topol.top, line 6147]
No default G96Angle types

and
Error 904 [file topol.top, line 6159]
No default Proper Dih. types

However, when I checked these lines I understood that
1- many of these bonds, angles, and dihedrals are related to atoms that are
not connected to each other, or
2- I have defined the appropriate bond, angle, or dihedral, but I do not
know why pdb2gmx didn't assign them.

you can see all the files via
https://www.dropbox.com/s/c8csnchfdahe016/4MEHR.zip?dl=0

Excuse me for my poor English,

Truly yours,
Farideh

On Wed, Sep 30, 2015 at 3:03 PM, Justin Lemkul  wrote:

>
>
> On 9/30/15 7:21 AM, faride badalkhani wrote:
>
>> Dear all,
>>
>> Could you tell me what is wrong when there are some strange bond, angles
>> and dihedrals in the topology file after executing pdb2gmx command?
>> for example atoms 1 and 27 do not have any connectivity, but pdb2gmx
>> generate them as [bonds]. A similar problem occurs in case of angles and
>> dihedrals.
>>
>>
> Impossible to say without knowing what you're actually doing.  Please
> always provide a full description of your system, your pdb2gmx command, and
> any relevant output, snippets of files, etc.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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[gmx-users] How OpenMP works with CUDA/GPU in Gromacs

[M Teguh Satria]

Hi All,

I am new in using Gromacs GPU. Anyone can help to explain me, how actually
OpenMP works with CUDA/GPU in Gromacs ? Or in which part of Gromacs that
OpenMP helps ?

Thanks in advance.

Regards,
Teguh

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Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Venkat Reddy]

Hi,
1) Yes, I can access the same xtc with older gromacs versions.
2) I can't access even smaller xtc files with 5.1
I will file a bug report for the same.
Thank you



On Wed, Sep 30, 2015 at 9:28 PM, Teemu Murtola 
wrote:

> Hi,
>
> This sounds like the build system is not compiling Gromacs with 64-bit file
> support like it should. Can you access the same file on the same system
> with earlier Gromacs versions? Can you access smaller files with 5.1?
>
> Could you file a bug report at redmine.gromacs.org, and include at least
> the following:
> * information on your operating system
> * contents of CMakeCache.txt, src/config.h, and src/gmxpre-config.h from
> your build tree
> * how you invoked cmake to configure the build.
>
> Teemu
>
> On Wed, Sep 30, 2015, 11:59 Venkat Reddy  wrote:
>
> > Hi Teemu,
> > Thanks for the prompt reply. Yes, the xtc file size is larger than 2GB
> > (approx. 50GB) and both system.xtc and traj.xtc are same files. I am
> > extremely sorry for the confusion :)
> >
> > On Wed, Sep 30, 2015 at 11:31 AM, Teemu Murtola  >
> > wrote:
> >
> > > Thanks for testing it, I see that there is still room for improvement
> in
> > > getting more context information into the error messages. I'm a bit
> > > confused by the difference between your original report of system.xtc
> vs
> > > traj.xtc in the new message, but that may not matter that much. Is your
> > xtc
> > > file larger that 2GB in size?
> > >
> > > On Wed, Sep 30, 2015, 07:53 Venkat Reddy  wrote:
> > >
> > > > Hi Teemu,
> > > > Thank you for providing the patch. But the patched version is giving
> > > > following error message:
> > > >
> > > > Program: gmx rdf, VERSION 5.2-dev
> > > > Source file: src/gromacs/utility/path.cpp (line 406)
> > > > Function:static void gmx::File::throwOnError(const
> > > > gmx::File::NotFoundInfo&)
> > > >
> > > > System I/O error:
> > > > Failed to access file 'traj.xtc'.
> > > > The file could not be opened.
> > > >   Reason: Value too large for defined data type
> > > >   (call to fopen() returned error code 75)
> > > >
> > > > I would like to inform you that I have installed this patched version
> > to
> > > a
> > > > non-standard location.
> > > >
> > > >
> > > > On Wed, Sep 30, 2015 at 8:39 AM, Teemu Murtola <
> > teemu.murt...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I now changed the check to provide more details (in 5140
> > > > > ). If you haven't figured out
> what
> > > the
> > > > > issue was, you could try building the source code from the above
> > link,
> > > > and
> > > > > running it to get more details.
> > > > >
> > > > > There is not much we can do to help diagnose the issue further,
> > unless
> > > > you
> > > > > can provide additional information on the file system contents.
> Also
> > > note
> > > > > that if you provide an input file name that looks like a valid file
> > > name
> > > > > (with the correct extension), Gromacs 5.1 will use it as is, or
> give
> > an
> > > > > error if it does not exist. Previous versions silently tried to
> > append
> > > > all
> > > > > kinds of extensions if the file did not exist (or could not be
> read)
> > > even
> > > > > in such a case, and could then use some other file as input.
> > > > >
> > > > > Best regards,
> > > > > Teemu
> > > > >
> > > > > On Sat, Sep 26, 2015 at 11:56 AM Teemu Murtola <
> > > teemu.murt...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > This error has nothing to do with the contents of the file, but
> > > rather
> > > > > the
> > > > > > operating system appears to be telling Gromacs that the file
> cannot
> > > be
> > > > > > opened or that it is not a regular file. With the information
> here,
> > > > it's
> > > > > > difficult to say anything more; if you want to debug this
> further,
> > > the
> > > > > > relevant function is gmx::File::exists().
> > > > > >
> > > > > > It would be useful to know what's the problem so that the check
> (or
> > > the
> > > > > > error message) can be improved.
> > > > > >
> > > > > > Best regards,
> > > > > > Teemu
> > > > > >
> > > > > > On Fri, Sep 25, 2015, 21:20 Venkat Reddy 
> > > wrote:
> > > > > >
> > > > > >> Hi Tsjerk,
> > > > > >> Thank you for the quick reply. Yes I can access it with other
> > > > versions,
> > > > > >> like 4.5.5, 5.0.4.
> > > > > >>
> > > > > >> On Fri, Sep 25, 2015 at 11:33 PM, Tsjerk Wassenaar <
> > > tsje...@gmail.com
> > > > >
> > > > > >> wrote:
> > > > > >>
> > > > > >> > Hi Venkat,
> > > > > >> >
> > > > > >> > Does it exist? Is it accessible? The XTC format did not change
> > > since
> > > > > the
> > > > > >> > early years of Gromacs. Can you access it with a different
> > > version?
> > > > > >> >
> > > > > >> > Cheers,
> > > > > >> >
> > > > > >> > Tsjerk
> > > > > >> > On Sep 25, 2015 19:52, "Venkat Reddy" 
> > > wrote:
> > > > > 

Re: [gmx-users] Simulations of proteins in membrane bilayer

[Terry]

Hi,

Try options '-pbc mol -center' with the gmx trjconv tool.

Terry


On Thu, Oct 1, 2015 at 4:48 AM, 凌未风  wrote:

> Hi All:
>
> I am doing a simulation in which a protein is inserted into a bilayer. In
> my simulations, the protein moved on the x-y plane of the bilayer (which is
> normal). However, in order to do some analysis, I have to put the protein
> to the center of the box, but still keep the box filled by lipids. Does
> anyone know how to do this?
> Of course, I could put the protein to the center of the box by align the
> protein with that in the first snapshot, but in this way, some of the
> lipids will be out of the PBC box. In my case, I have to keep all of the
> lipids in the PBC box and packed around the protein.
>
> I am really appreciate for your suggestions and help.
>
> With my best regards,
> RXG
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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Re: [gmx-users] bond, angles and dihedrals in the topology file

[faride badalkhani]

Dear Chandan,
Thanks a lot for your answer.
Truly yours,
Farideh

On Wednesday, September 30, 2015, Chandan Choudhury 
wrote:
> Dear Farideh,
>
> You may have a look at
>
https://code.google.com/p/molecular-simulation-of-soft-matter/issues/detail?id=1
> for one such example.
>
> Chandan
>
> On Wed, Sep 30, 2015 at 8:29 PM, faride badalkhani <
> farideh.kham...@gmail.com> wrote:
>
>> Thank you for your time and answer. You are right, Dendrimers are
composed
>> of three main architectural components, a central core from which
multiple
>> arms emanate in an outward direction to form interior layers, and the
>> reactive peripheral surface groups. Could you tell me if there is a
sample
>> specbond file for hyperbranched polymers?
>>
>> Regards,
>> Farideh
>>
>> On Wed, Sep 30, 2015 at 6:07 PM, Justin Lemkul  wrote:
>>
>> >
>> >
>> > On 9/30/15 8:24 AM, faride badalkhani wrote:
>> >
>> >> I want to simulate a dendrimer (a hyperbranched polymer) in water. I
>> have
>> >> used the GROMOS 53A6 force field parameters, and I have done the
>> following
>> >> steps:
>> >> 1- Defining new atom types that were not exist in .atp file.
>> >> 2- Adding appropriate bonds, angles, dihedrals, and impropers into the
>> >> ffbonded.itp file.
>> >> 3- Defining nonbonded parameters in ffnonbonded.itp file according to
>> >> GROMOS FF parameters.
>> >> 4- Introducing residue building blocks along with [bonds], [angles],
>> >> [impropers], and [dihedrals] in .rtp file.
>> >>
>> >> After using pdb2gmx I receive this command:
>> >>
>> >> You have successfully generated a topology from: g3n.pdb
>> >> The CA force field and the spce water model are used.
>> >>
>> >> Then I define box and solvent without any problems, but there are many
>> >> errors when I execute grompp command as follows:
>> >> Error 892 [file topol.top, line 6147]
>> >> No default G96Angle types
>> >>
>> >> and
>> >> Error 904 [file topol.top, line 6159]
>> >> No default Proper Dih. types
>> >>
>> >> However, when I checked these lines I understood that
>> >> 1- many of these bonds, angles, and dihedrals are related to atoms
that
>> >> are
>> >> not connected to each other, or
>> >> 2- I have defined the appropriate bond, angle, or dihedral, but I do
not
>> >> know why pdb2gmx didn't assign them.
>> >>
>> >> you can see all the files via
>> >> https://www.dropbox.com/s/c8csnchfdahe016/4MEHR.zip?dl=0
>> >>
>> >>
>> > Indeed, you have many missing interactions. This means you either have
>> not
>> > added all of the necessary interactions that you think you have, or
your
>> > connectivity is wrong. It could even be both. Just looking at the first
>> > three residues, you have bonds between residues 1-2 and 1-3. pdb2gmx
>> won't
>> > support this; your .rtp files can only specify bonds between
consecutive
>> > residues via the +/- mechanism. So you're probably getting some
>> unexpected
>> > connectivity. I don't see any bond between atoms 1 and 27 as your first
>> > message claimed. You may be able to get specbond.dat to work somehow
>> here,
>> > as that is the only way to assign bonds between non-consecutive
residues.
>> >
>> > -Justin
>> >
>> >
>> > Excuse me for my poor English,
>> >>
>> >> Truly yours,
>> >> Farideh
>> >>
>> >> On Wed, Sep 30, 2015 at 3:03 PM, Justin Lemkul 
wrote:
>> >>
>> >>
>> >>>
>> >>> On 9/30/15 7:21 AM, faride badalkhani wrote:
>> >>>
>> >>> Dear all,
>> 
>>  Could you tell me what is wrong when there are some strange bond,
>> angles
>>  and dihedrals in the topology file after executing pdb2gmx command?
>>  for example atoms 1 and 27 do not have any connectivity, but pdb2gmx
>>  generate them as [bonds]. A similar problem occurs in case of angles
>> and
>>  dihedrals.
>> 
>> 
>>  Impossible to say without knowing what you're actually doing.
Please
>> >>> always provide a full description of your system, your pdb2gmx
command,
>> >>> and
>> >>> any relevant output, snippets of files, etc.
>> >>>
>> >>> -Justin
>> >>>
>> >>> --
>> >>> ==
>> >>>
>> >>> Justin A. Lemkul, Ph.D.
>> >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> >>>
>> >>> Department of Pharmaceutical Sciences
>> >>> School of Pharmacy
>> >>> Health Sciences Facility II, Room 629
>> >>> University of Maryland, Baltimore
>> >>> 20 Penn St.
>> >>> Baltimore, MD 21201
>> >>>
>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> >>> http://mackerell.umaryland.edu/~jalemkul
>> >>>
>> >>> ==
>> >>> --
>> >>> Gromacs Users mailing list
>> >>>
>> >>> * Please search the archive at
>> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> >>> posting!
>> >>>
>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>>
>> >>> * For (un)subscribe requests visit
>> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> >>> send a mail to 

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Teemu Murtola]

Are you saying that you cannot open any xtc files? If that is the case,
then this may not have anything to do with 64-bit for support. Can your
Gromacs compilation open any files? You will need to isolate the problem a
bit to help diagnosing it, since we don't have access to your system.

Teemu

On Thu, Oct 1, 2015, 07:48 Venkat Reddy  wrote:

> Hi,
> 1) Yes, I can access the same xtc with older gromacs versions.
> 2) I can't access even smaller xtc files with 5.1
> I will file a bug report for the same.
> Thank you
>
>
>
> On Wed, Sep 30, 2015 at 9:28 PM, Teemu Murtola 
> wrote:
>
> > Hi,
> >
> > This sounds like the build system is not compiling Gromacs with 64-bit
> file
> > support like it should. Can you access the same file on the same system
> > with earlier Gromacs versions? Can you access smaller files with 5.1?
> >
> > Could you file a bug report at redmine.gromacs.org, and include at least
> > the following:
> > * information on your operating system
> > * contents of CMakeCache.txt, src/config.h, and src/gmxpre-config.h from
> > your build tree
> > * how you invoked cmake to configure the build.
> >
> > Teemu
> >
> > On Wed, Sep 30, 2015, 11:59 Venkat Reddy  wrote:
> >
> > > Hi Teemu,
> > > Thanks for the prompt reply. Yes, the xtc file size is larger than 2GB
> > > (approx. 50GB) and both system.xtc and traj.xtc are same files. I am
> > > extremely sorry for the confusion :)
> > >
> > > On Wed, Sep 30, 2015 at 11:31 AM, Teemu Murtola <
> teemu.murt...@gmail.com
> > >
> > > wrote:
> > >
> > > > Thanks for testing it, I see that there is still room for improvement
> > in
> > > > getting more context information into the error messages. I'm a bit
> > > > confused by the difference between your original report of system.xtc
> > vs
> > > > traj.xtc in the new message, but that may not matter that much. Is
> your
> > > xtc
> > > > file larger that 2GB in size?
> > > >
> > > > On Wed, Sep 30, 2015, 07:53 Venkat Reddy 
> wrote:
> > > >
> > > > > Hi Teemu,
> > > > > Thank you for providing the patch. But the patched version is
> giving
> > > > > following error message:
> > > > >
> > > > > Program: gmx rdf, VERSION 5.2-dev
> > > > > Source file: src/gromacs/utility/path.cpp (line 406)
> > > > > Function:static void gmx::File::throwOnError(const
> > > > > gmx::File::NotFoundInfo&)
> > > > >
> > > > > System I/O error:
> > > > > Failed to access file 'traj.xtc'.
> > > > > The file could not be opened.
> > > > >   Reason: Value too large for defined data type
> > > > >   (call to fopen() returned error code 75)
> > > > >
> > > > > I would like to inform you that I have installed this patched
> version
> > > to
> > > > a
> > > > > non-standard location.
> > > > >
> > > > >
> > > > > On Wed, Sep 30, 2015 at 8:39 AM, Teemu Murtola <
> > > teemu.murt...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > I now changed the check to provide more details (in 5140
> > > > > > ). If you haven't figured out
> > what
> > > > the
> > > > > > issue was, you could try building the source code from the above
> > > link,
> > > > > and
> > > > > > running it to get more details.
> > > > > >
> > > > > > There is not much we can do to help diagnose the issue further,
> > > unless
> > > > > you
> > > > > > can provide additional information on the file system contents.
> > Also
> > > > note
> > > > > > that if you provide an input file name that looks like a valid
> file
> > > > name
> > > > > > (with the correct extension), Gromacs 5.1 will use it as is, or
> > give
> > > an
> > > > > > error if it does not exist. Previous versions silently tried to
> > > append
> > > > > all
> > > > > > kinds of extensions if the file did not exist (or could not be
> > read)
> > > > even
> > > > > > in such a case, and could then use some other file as input.
> > > > > >
> > > > > > Best regards,
> > > > > > Teemu
> > > > > >
> > > > > > On Sat, Sep 26, 2015 at 11:56 AM Teemu Murtola <
> > > > teemu.murt...@gmail.com>
> > > > > > wrote:
> > > > > >
> > > > > > > This error has nothing to do with the contents of the file, but
> > > > rather
> > > > > > the
> > > > > > > operating system appears to be telling Gromacs that the file
> > cannot
> > > > be
> > > > > > > opened or that it is not a regular file. With the information
> > here,
> > > > > it's
> > > > > > > difficult to say anything more; if you want to debug this
> > further,
> > > > the
> > > > > > > relevant function is gmx::File::exists().
> > > > > > >
> > > > > > > It would be useful to know what's the problem so that the check
> > (or
> > > > the
> > > > > > > error message) can be improved.
> > > > > > >
> > > > > > > Best regards,
> > > > > > > Teemu
> > > > > > >
> > > > > > > On Fri, Sep 25, 2015, 21:20 Venkat Reddy 
> > > > wrote:
> > > > > > >
> > > > > > >> Hi Tsjerk,
> > > > > > >> Thank you for 

Re: [gmx-users] bond, angles and dihedrals in the topology file

[faride badalkhani]

Thank you for your time and answer. You are right, Dendrimers are composed
of three main architectural components, a central core from which multiple
arms emanate in an outward direction to form interior layers, and the
reactive peripheral surface groups. Could you tell me if there is a sample
specbond file for hyperbranched polymers?

Regards,
Farideh

On Wed, Sep 30, 2015 at 6:07 PM, Justin Lemkul  wrote:

>
>
> On 9/30/15 8:24 AM, faride badalkhani wrote:
>
>> I want to simulate a dendrimer (a hyperbranched polymer) in water. I have
>> used the GROMOS 53A6 force field parameters, and I have done the following
>> steps:
>> 1- Defining new atom types that were not exist in .atp file.
>> 2- Adding appropriate bonds, angles, dihedrals, and impropers into the
>> ffbonded.itp file.
>> 3- Defining nonbonded parameters in ffnonbonded.itp file according to
>> GROMOS FF parameters.
>> 4- Introducing residue building blocks along with [bonds], [angles],
>> [impropers], and [dihedrals] in .rtp file.
>>
>> After using pdb2gmx I receive this command:
>>
>> You have successfully generated a topology from: g3n.pdb
>> The CA force field and the spce water model are used.
>>
>> Then I define box and solvent without any problems, but there are many
>> errors when I execute grompp command as follows:
>> Error 892 [file topol.top, line 6147]
>> No default G96Angle types
>>
>> and
>> Error 904 [file topol.top, line 6159]
>> No default Proper Dih. types
>>
>> However, when I checked these lines I understood that
>> 1- many of these bonds, angles, and dihedrals are related to atoms that
>> are
>> not connected to each other, or
>> 2- I have defined the appropriate bond, angle, or dihedral, but I do not
>> know why pdb2gmx didn't assign them.
>>
>> you can see all the files via
>> https://www.dropbox.com/s/c8csnchfdahe016/4MEHR.zip?dl=0
>>
>>
> Indeed, you have many missing interactions. This means you either have not
> added all of the necessary interactions that you think you have, or your
> connectivity is wrong. It could even be both. Just looking at the first
> three residues, you have bonds between residues 1-2 and 1-3. pdb2gmx won't
> support this; your .rtp files can only specify bonds between consecutive
> residues via the +/- mechanism. So you're probably getting some unexpected
> connectivity. I don't see any bond between atoms 1 and 27 as your first
> message claimed. You may be able to get specbond.dat to work somehow here,
> as that is the only way to assign bonds between non-consecutive residues.
>
> -Justin
>
>
> Excuse me for my poor English,
>>
>> Truly yours,
>> Farideh
>>
>> On Wed, Sep 30, 2015 at 3:03 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 9/30/15 7:21 AM, faride badalkhani wrote:
>>>
>>> Dear all,

 Could you tell me what is wrong when there are some strange bond, angles
 and dihedrals in the topology file after executing pdb2gmx command?
 for example atoms 1 and 27 do not have any connectivity, but pdb2gmx
 generate them as [bonds]. A similar problem occurs in case of angles and
 dihedrals.


 Impossible to say without knowing what you're actually doing.  Please
>>> always provide a full description of your system, your pdb2gmx command,
>>> and
>>> any relevant output, snippets of files, etc.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> 

Re: [gmx-users] bond, angles and dihedrals in the topology file

[Justin Lemkul]

On 9/30/15 8:24 AM, faride badalkhani wrote:

I want to simulate a dendrimer (a hyperbranched polymer) in water. I have
used the GROMOS 53A6 force field parameters, and I have done the following
steps:
1- Defining new atom types that were not exist in .atp file.
2- Adding appropriate bonds, angles, dihedrals, and impropers into the
ffbonded.itp file.
3- Defining nonbonded parameters in ffnonbonded.itp file according to
GROMOS FF parameters.
4- Introducing residue building blocks along with [bonds], [angles],
[impropers], and [dihedrals] in .rtp file.

After using pdb2gmx I receive this command:

You have successfully generated a topology from: g3n.pdb
The CA force field and the spce water model are used.

Then I define box and solvent without any problems, but there are many
errors when I execute grompp command as follows:
Error 892 [file topol.top, line 6147]
No default G96Angle types

and
Error 904 [file topol.top, line 6159]
No default Proper Dih. types

However, when I checked these lines I understood that
1- many of these bonds, angles, and dihedrals are related to atoms that are
not connected to each other, or
2- I have defined the appropriate bond, angle, or dihedral, but I do not
know why pdb2gmx didn't assign them.

you can see all the files via
https://www.dropbox.com/s/c8csnchfdahe016/4MEHR.zip?dl=0



Indeed, you have many missing interactions. This means you either have not added 
all of the necessary interactions that you think you have, or your connectivity 
is wrong. It could even be both. Just looking at the first three residues, you 
have bonds between residues 1-2 and 1-3. pdb2gmx won't support this; your .rtp 
files can only specify bonds between consecutive residues via the +/- mechanism. 
So you're probably getting some unexpected connectivity. I don't see any bond 
between atoms 1 and 27 as your first message claimed. You may be able to get 
specbond.dat to work somehow here, as that is the only way to assign bonds 
between non-consecutive residues.


-Justin


Excuse me for my poor English,

Truly yours,
Farideh

On Wed, Sep 30, 2015 at 3:03 PM, Justin Lemkul  wrote:




On 9/30/15 7:21 AM, faride badalkhani wrote:


Dear all,

Could you tell me what is wrong when there are some strange bond, angles
and dihedrals in the topology file after executing pdb2gmx command?
for example atoms 1 and 27 do not have any connectivity, but pdb2gmx
generate them as [bonds]. A similar problem occurs in case of angles and
dihedrals.



Impossible to say without knowing what you're actually doing.  Please
always provide a full description of your system, your pdb2gmx command, and
any relevant output, snippets of files, etc.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] gmx distance lipid bilayer

[Repic Matej]

As said, you are not measuring what you presumably want. As I understand,
you should be measuring the distance between the com of P atoms from the
same _monolayer_ and the com of all lipids (or all P atoms of the
bilayer). This way, the first com will be in the middle of the plane
formed by the P atoms in one monolayer, and the other com will be in the
middle of the plane at the interface between top and bottom bilayers. This
distance should be similar to the length of the acyl chain.

It is customary to measure the membrane thickness in lipid simulations as
P-P distance, so I suggest you make top and bottom P groups in a ndx file
and measure the distance between the two centers of mass. This value can
also be compared to experiment to validate the simulation.

Best,

--
Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC ­ LCBC
BCH 4108
CH - 1015 Lausanne
--







On 9/30/15, 17:20, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Justin Lemkul"
 wrote:

>
>
>On 9/30/15 11:17 AM, xy21hb wrote:
>> Dear all,
>>
>> I am using gmx distance to calculate the distance between the center of
>>mass (c.o.m.) of the phosphorous group (PO4, 5 atoms)
>> and the c.o.m. of the lipid bilayer system in Justin's tutorial (a
>>typical lipid DPPC bilayer system) by issuing, as shown on GROMACS
>>website for gmx distance,
>>
>> gmx distance -n index.ndx -select 'com of group "A" plus com of group
>>"B"' -oxyz -oall -s md.tpr -f md.trr
>>
>> where A = Phsphorous B = System.
>>
>> The distance should be about the chain length of the lipid, so ~ 20 A
>>
>> However, it gives ~ 0.1 nm. I just wonder why it is like that.
>>
>
>Because your assumption is wrong.  The bilayer is centered in the box, so
>the 
>COM distance between the center of the system and the center of the P
>atoms is 
>usually about the same position, so you get a value that is nearly zero.
>
>-Justin
>
>-- 
>==
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalem...@outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==
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>posting!
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[gmx-users] gmx distance lipid bilayer

[xy21hb]

Dear all,

I am using gmx distance to calculate the distance between the center of mass 
(c.o.m.) of the phosphorous group (PO4, 5 atoms)
and the c.o.m. of the lipid bilayer system in Justin's tutorial (a typical 
lipid DPPC bilayer system) by issuing, as shown on GROMACS website for gmx 
distance,

gmx distance -n index.ndx -select 'com of group "A" plus com of group "B"' 
-oxyz -oall -s md.tpr -f md.trr

where A = Phsphorous B = System.

The distance should be about the chain length of the lipid, so ~ 20 A

However, it gives ~ 0.1 nm. I just wonder why it is like that.

Many thanks,

Yao





 
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[gmx-users] gmx distance lipid bilayer

[xy21hb]

Dear all,

I am using gmx distance to calculate the distance between the center of mass 
(c.o.m.) of the phosphorous group (PO4, 5 atoms)
and the c.o.m. of the lipid bilayer system in Justin's tutorial (a typical 
lipid DPPC bilayer system) by issuing, as shown on GROMACS website for gmx 
distance,

gmx distance -n index.ndx -select 'com of group "A" plus com of group "B"' 
-oxyz -oall -s md.tpr -f md.trr

where A = Phsphorous B = System.

The distance should be about the chain length of the lipid, so ~ 20 A

However, it gives ~ 0.1 nm. I just wonder why it is like that.

Many thanks,

Yao
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[gmx-users] Fw: gmx distance lipid bilayer

[xy21hb]

Dear all,

However, even if I choose B = C16 (last Carbon atom of sn-1 chain), it gives 
similar result.
Then I wonder how I could get the distance of my interest.

Thanks,

Yao









At 2015-09-30 23:20:28, "Justin Lemkul"  wrote:
>
>
>On 9/30/15 11:17 AM, xy21hb wrote:
>> Dear all,
>>
>> I am using gmx distance to calculate the distance between the center of mass 
>> (c.o.m.) of the phosphorous group (PO4, 5 atoms)
>> and the c.o.m. of the lipid bilayer system in Justin's tutorial (a typical 
>> lipid DPPC bilayer system) by issuing, as shown on GROMACS website for gmx 
>> distance,
>>
>> gmx distance -n index.ndx -select 'com of group "A" plus com of group "B"' 
>> -oxyz -oall -s md.tpr -f md.trr
>>
>> where A = Phsphorous B = System.
>>
>> The distance should be about the chain length of the lipid, so ~ 20 A
>>
>> However, it gives ~ 0.1 nm. I just wonder why it is like that.
>>
>
>Because your assumption is wrong.  The bilayer is centered in the box, so the 
>COM distance between the center of the system and the center of the P atoms is 
>usually about the same position, so you get a value that is nearly zero.
>
>-Justin
>
>-- 
>==
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalem...@outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==
>-- 
>Gromacs Users mailing list
>
>* Please search the archive at 
>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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>mail to gmx-users-requ...@gromacs.org.





 
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Re: [gmx-users] gmx distance lipid bilayer

[xy21hb]

Dear all,

However, even if I choose B = C16 (last Carbon atom of sn-1 chain), it gives 
similar result.
Then I wonder how I could get the distance of my interest.

Thanks,

Yao









At 2015-09-30 23:20:28, "Justin Lemkul"  wrote:
>
>
>On 9/30/15 11:17 AM, xy21hb wrote:
>> Dear all,
>>
>> I am using gmx distance to calculate the distance between the center of mass 
>> (c.o.m.) of the phosphorous group (PO4, 5 atoms)
>> and the c.o.m. of the lipid bilayer system in Justin's tutorial (a typical 
>> lipid DPPC bilayer system) by issuing, as shown on GROMACS website for gmx 
>> distance,
>>
>> gmx distance -n index.ndx -select 'com of group "A" plus com of group "B"' 
>> -oxyz -oall -s md.tpr -f md.trr
>>
>> where A = Phsphorous B = System.
>>
>> The distance should be about the chain length of the lipid, so ~ 20 A
>>
>> However, it gives ~ 0.1 nm. I just wonder why it is like that.
>>
>
>Because your assumption is wrong.  The bilayer is centered in the box, so the 
>COM distance between the center of the system and the center of the P atoms is 
>usually about the same position, so you get a value that is nearly zero.
>
>-Justin
>
>-- 
>==
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalem...@outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==
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>Gromacs Users mailing list
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>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Teemu Murtola]

Hi,

This sounds like the build system is not compiling Gromacs with 64-bit file
support like it should. Can you access the same file on the same system
with earlier Gromacs versions? Can you access smaller files with 5.1?

Could you file a bug report at redmine.gromacs.org, and include at least
the following:
* information on your operating system
* contents of CMakeCache.txt, src/config.h, and src/gmxpre-config.h from
your build tree
* how you invoked cmake to configure the build.

Teemu

On Wed, Sep 30, 2015, 11:59 Venkat Reddy  wrote:

> Hi Teemu,
> Thanks for the prompt reply. Yes, the xtc file size is larger than 2GB
> (approx. 50GB) and both system.xtc and traj.xtc are same files. I am
> extremely sorry for the confusion :)
>
> On Wed, Sep 30, 2015 at 11:31 AM, Teemu Murtola 
> wrote:
>
> > Thanks for testing it, I see that there is still room for improvement in
> > getting more context information into the error messages. I'm a bit
> > confused by the difference between your original report of system.xtc vs
> > traj.xtc in the new message, but that may not matter that much. Is your
> xtc
> > file larger that 2GB in size?
> >
> > On Wed, Sep 30, 2015, 07:53 Venkat Reddy  wrote:
> >
> > > Hi Teemu,
> > > Thank you for providing the patch. But the patched version is giving
> > > following error message:
> > >
> > > Program: gmx rdf, VERSION 5.2-dev
> > > Source file: src/gromacs/utility/path.cpp (line 406)
> > > Function:static void gmx::File::throwOnError(const
> > > gmx::File::NotFoundInfo&)
> > >
> > > System I/O error:
> > > Failed to access file 'traj.xtc'.
> > > The file could not be opened.
> > >   Reason: Value too large for defined data type
> > >   (call to fopen() returned error code 75)
> > >
> > > I would like to inform you that I have installed this patched version
> to
> > a
> > > non-standard location.
> > >
> > >
> > > On Wed, Sep 30, 2015 at 8:39 AM, Teemu Murtola <
> teemu.murt...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > I now changed the check to provide more details (in 5140
> > > > ). If you haven't figured out what
> > the
> > > > issue was, you could try building the source code from the above
> link,
> > > and
> > > > running it to get more details.
> > > >
> > > > There is not much we can do to help diagnose the issue further,
> unless
> > > you
> > > > can provide additional information on the file system contents. Also
> > note
> > > > that if you provide an input file name that looks like a valid file
> > name
> > > > (with the correct extension), Gromacs 5.1 will use it as is, or give
> an
> > > > error if it does not exist. Previous versions silently tried to
> append
> > > all
> > > > kinds of extensions if the file did not exist (or could not be read)
> > even
> > > > in such a case, and could then use some other file as input.
> > > >
> > > > Best regards,
> > > > Teemu
> > > >
> > > > On Sat, Sep 26, 2015 at 11:56 AM Teemu Murtola <
> > teemu.murt...@gmail.com>
> > > > wrote:
> > > >
> > > > > This error has nothing to do with the contents of the file, but
> > rather
> > > > the
> > > > > operating system appears to be telling Gromacs that the file cannot
> > be
> > > > > opened or that it is not a regular file. With the information here,
> > > it's
> > > > > difficult to say anything more; if you want to debug this further,
> > the
> > > > > relevant function is gmx::File::exists().
> > > > >
> > > > > It would be useful to know what's the problem so that the check (or
> > the
> > > > > error message) can be improved.
> > > > >
> > > > > Best regards,
> > > > > Teemu
> > > > >
> > > > > On Fri, Sep 25, 2015, 21:20 Venkat Reddy 
> > wrote:
> > > > >
> > > > >> Hi Tsjerk,
> > > > >> Thank you for the quick reply. Yes I can access it with other
> > > versions,
> > > > >> like 4.5.5, 5.0.4.
> > > > >>
> > > > >> On Fri, Sep 25, 2015 at 11:33 PM, Tsjerk Wassenaar <
> > tsje...@gmail.com
> > > >
> > > > >> wrote:
> > > > >>
> > > > >> > Hi Venkat,
> > > > >> >
> > > > >> > Does it exist? Is it accessible? The XTC format did not change
> > since
> > > > the
> > > > >> > early years of Gromacs. Can you access it with a different
> > version?
> > > > >> >
> > > > >> > Cheers,
> > > > >> >
> > > > >> > Tsjerk
> > > > >> > On Sep 25, 2015 19:52, "Venkat Reddy" 
> > wrote:
> > > > >> >
> > > > >> > > Dear all,
> > > > >> > > I have a trajectory file generated by gromacs-4.5.5. Recently
> I
> > > > tried
> > > > >> to
> > > > >> > > plot radial distribution function using 'gmx rdf' tool
> available
> > > in
> > > > >> > > gromacs-5.1. But I am getting the following error.
> > > > >> > > Error in user input:
> > > > >> > > Invalid command-line options
> > > > >> > >   In command-line option -f
> > > > >> > > File 'system.xtc' does not exist or is not accessible.
> > > > >> > >
> > > > >> > > I knew that gromacs 

Re: [gmx-users] gmx distance lipid bilayer

[Justin Lemkul]

On 9/30/15 11:17 AM, xy21hb wrote:

Dear all,

I am using gmx distance to calculate the distance between the center of mass 
(c.o.m.) of the phosphorous group (PO4, 5 atoms)
and the c.o.m. of the lipid bilayer system in Justin's tutorial (a typical 
lipid DPPC bilayer system) by issuing, as shown on GROMACS website for gmx 
distance,

gmx distance -n index.ndx -select 'com of group "A" plus com of group "B"' 
-oxyz -oall -s md.tpr -f md.trr

where A = Phsphorous B = System.

The distance should be about the chain length of the lipid, so ~ 20 A

However, it gives ~ 0.1 nm. I just wonder why it is like that.



Because your assumption is wrong.  The bilayer is centered in the box, so the 
COM distance between the center of the system and the center of the P atoms is 
usually about the same position, so you get a value that is nearly zero.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Atom OXT in PHE

[Sepideh Kavousi]

Hi,
In the force fiels that you use this atom in not introduced. you have to
import the information of atom in the atomtypes.atp file in the related
force field you use

On Sun, Sep 27, 2015 at 2:15 AM, Amali Guruge  wrote:

> Dear all,
>
>
> When I give pdb2gmx command I got the following error.
>
> Atom OXT in residue PHE 765 was not found in rtp entry PHE with 20 atoms
> while sorting.
>
> How can I fix this problem? Can anyone help me?
>
> Thank you...
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