[gmx-users] Re: Extending the simulation

[bharat gupta]

Hi,

I extended by 3ns simulation by 2 more ns ... i.e total 5 ns but the .xtc
file shows only the 3ns trajectories and after checking the md.log file ,
its showing that it completed those 2 ns steps also... then how can I get
the trajectory for those 2ns ... I used the following commands for extending
the simulation ...

tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt


-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
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Re: [gmx-users] PRODRG

[mohsen ramezanpour]

Dear Dr.Justin

I did it,it works.Thanks.

there are another problem:
I want to add some hydogens to my topology.
I used ADDHYD atomname,But this dosen't work.
PLease let me know how can I include some Hydrogenes in my topology.
Thanks in advance
Mohsen

On Thu, Feb 10, 2011 at 7:56 PM, Justin A. Lemkul  wrote:

>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> I have read this section before.
>> There are 2 problem:
>> 1:ADDHYD atomname and DELHYD atomname  commands dosen't work!
>> they result in ERROR in PRODRG
>>
>>
> You have to run PRODRG twice.  The first time, you get the wrong output.
>  Note the atom name that PRODRG assigns to your N atom.  The second time,
> use DELHYD (name).  If that doesn't work, then I have no idea and you're
> better off submitting your question to the PRODRG developers.
>
>
>  2:Actually I don't know the additional hydrogen is necessary or not!
>> Because it may be necessary for proper protonation.
>> My drug(Sertraline) is in a solvent,it may interact with water molecules
>> and Nitrogen may  get an additional hydrogen.
>>
>>
> A doubly-protonated secondary amine would be a fairly strong acid.  You
> should do a pKa calculation to determine what is relevant rather than
> guessing.  There are web servers and other software out there that can do
> this for you.  Google is your friend.
>
> -Justin
>
>  What do you think?
>>
>>
>>
>> On Wed, Feb 9, 2011 at 9:39 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>The OP's question is easily answered by referring to the PRODRG FAQ
>>in dealing with proper protonation.
>>
>>As for Antechamber and the like, these are good tools, but do not
>>produce GROMOS-compatible topologies, if that is indeed the
>>underlying goal.  We've done thorough analysis of various QM
>>calculation methods for GROMOS charges, and none of them produce
>>completely satisfactory topologies.  Antechamber, Spartan, Gaussian,
>>etc are good for initial charge calculations, but IMHO do not
>>qualify as an "end result" for GROMOS parameterization due to the
>>empirical refinement used in the force field derivation.  All of
>>that makes GROMOS parameterization somewhat tricky, and hence why
>>force field choice is so incredibly important when designing
>>projects... ;)
>>
>>-Justin
>>
>>
>>TJ Mustard wrote:
>>
>>
>>
>>Yes I would recommend acpype.
>>
>>On February 9, 2011 at 9:42 AM
>>jorge_quint...@ciencias.uis.edu.co
>> wrote:
>>
>> > I think that is better to use antechamber tools.
>> >
>> >
>> > > On 10/02/2011 3:40 AM, mohsen ramezanpour wrote:
>> > >> Dear Users
>> > >>
>> > >> I am using PRODRG to make topology for my drug
>> > >> It addes Hydrogenes but in wrong way.
>> > >> My Nitrogen atom is bonded to 2 Carbos,
>> > >> and PRODRG addes 2 Hydrogenes to it .
>> > >> Please let me know how can I do.
>> > >> Thanks in advance
>> > >
>> > > This is not really the forum to get help about that. You
>>need to read
>> > > how to PRODRG needs input, and supply something it can deal
>>with. Then
>> > > do a whole bunch more work testing what it produced.
>> > >
>> > > Mark
>> > > --
>> > > gmx-users mailing listgmx-users@gromacs.org
>>
>>
>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > > Please search the archive at
>> > > http://www.gromacs.org/Support/Mailing_Lists/Search before
>>posting!
>> > > Please don't post (un)subscribe requests to the list. Use the
>> > > www interface or send it to gmx-users-requ...@gromacs.org
>>.
>>
>> > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > >
>> >
>> >
>> > --
>> > Jorge R. Quintero
>> > Químico
>> > Universidad Industrial de Santander
>> > Bucaramanga, Santander - Colombia
>> >
>> > --
>> > gmx-users mailing listgmx-users@gromacs.org
>>
>>
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at
>>http://www.gromacs.org/Support/Mailing_Lists/Search before
>> posting!
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-requ...@gromacs.org
>>.
>>
>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>>
>> TJ Mustard
>>Email: musta...@onid.orst.edu 
>>
>>
>>
>>-- 
>>
>>Justin A. Lemkul

[gmx-users] Re: crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning (Mark Abraham)

[Sanjay Kumar Upadhyay]

"iso-8859-1"
>
> Hi,
>
> I extended by 3ns simulation by 2 more ns ... i.e total 5 ns but the .xtc
> file shows only the 3ns trajectories and after checking the md.log file ,
> its showing that it completed those 2 ns steps also... then how can I get
> the trajectory for those 2ns ... I used the following commands for
> extending
> the simulation ...
>
> tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
> mdrun -s next.tpr -cpi previous.cpt
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46...@yahoo.com
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110210/94adb6d8/attachment-0001.html
>
> --
>
> Message: 3
> Date: Fri, 11 Feb 2011 08:55:01 +0100
> From: David van der Spoel 
> Subject: [gmx-users] Fwd: Question on Gromacs: rlist, rvdw, rcoulomb
> To: Discussion list for GROMACS users 
> Cc: Qin Qiao 
> Message-ID: <4d54eb55.6080...@xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> I am a user of gromacs. I am quite confused when I came across the
> relation of rlist and rvdw / rcoulomb in vdw and coulomb calculation.
>
> In cut-off, it says rvdw / rcoulomb should be greater than rlist, while
> in switch/shift, it says rvdw should be smaller than rlist...
>
> I guess in cut-off, it's to get all the updated atoms in the calculation
> of vdw/ coulomb by setting rvdw/ rcoulomb greater, but why it's the
> opposite in switch...
>
> Could you help me to understand how it's done? Thanks a lot.
>
> Best,
>
> Qin
>
>
> --
>
> Message: 4
> Date: Fri, 11 Feb 2011 01:10:54 -0800
> From: bharat gupta 
> Subject: [gmx-users] Re: Extending the simulation
> To: Discussion list for GROMACS users 
> Message-ID:
>   
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I extended by 3ns simulation by 2 more ns ... i.e total 5 ns but the .xtc
> file shows only the 3ns trajectories and after checking the md.log file ,
> its showing that it completed those 2 ns steps also... then how can I get
> the trajectory for those 2ns ... I used the following commands for
> extending
> the simulation ...
>
> tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
> mdrun -s next.tpr -cpi previous.cpt
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46...@yahoo.com
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110211/8d0e575f/attachment-0001.html
>
> --
>
> Message: 5
> Date: Fri, 11 Feb 2011 12:48:31 +0330
> From: mohsen ramezanpour 
> Subject: Re: [gmx-users] PRODRG
> To: jalem...@vt.edu, Discussion list for GROMACS users
>   
> Message-ID:
>   
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Dr.Justin
>
> I did it,it works.Thanks.
>
> there are another problem:
> I want to add some hydogens to my topology.
> I used ADDHYD atomname,But this dosen't work.
> PLease let me know how can I include some Hydrogenes in my topology.
> Thanks in advance
> Mohsen
>
> On Thu, Feb 10, 2011 at 7:56 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> mohsen ramezanpour wrote:
>>
>>> Dear Dr.Justin
>>>
>>> I have read this section before.
>>> There are 2 problem:
>>> 1:ADDHYD atomname and DELHYD atomname  commands dosen't work!
>>> they result in ERROR in PRODRG
>>>
>>>
>> You have to run PRODRG twice.  The first time, you get the wrong output.
>>  Note the atom name that PRODRG assigns to your N atom.  The second
>> time,
>> use DELHYD (name).  If that doesn't work, then I have no idea and you're
>> better off submitting your question to the PRODRG developers.
>>
>>
>>  2:Actually I don't know the additional hydrogen is necessary or not!
>>> Because it may be necessary for proper protonation.
>>> My 

Re: [gmx-users] PRODRG

[Justin A. Lemkul]

mohsen ramezanpour wrote:

Dear Dr.Justin

I did it,it works.Thanks.

there are another problem:
I want to add some hydogens to my topology.
I used ADDHYD atomname,But this dosen't work.
PLease let me know how can I include some Hydrogenes in my topology.


Use a different force field and don't use PRODRG.  Gromos96 is a united-atom 
force field.


-Justin


Thanks in advance
Mohsen

On Thu, Feb 10, 2011 at 7:56 PM, Justin A. Lemkul > wrote:




mohsen ramezanpour wrote:

Dear Dr.Justin

I have read this section before.
There are 2 problem:
1:ADDHYD atomname and DELHYD atomname  commands dosen't work!
they result in ERROR in PRODRG


You have to run PRODRG twice.  The first time, you get the wrong
output.  Note the atom name that PRODRG assigns to your N atom.  The
second time, use DELHYD (name).  If that doesn't work, then I have
no idea and you're better off submitting your question to the PRODRG
developers.


2:Actually I don't know the additional hydrogen is necessary or not!
Because it may be necessary for proper protonation.
My drug(Sertraline) is in a solvent,it may interact with water
molecules and Nitrogen may  get an additional hydrogen.


A doubly-protonated secondary amine would be a fairly strong acid.
 You should do a pKa calculation to determine what is relevant
rather than guessing.  There are web servers and other software out
there that can do this for you.  Google is your friend.

-Justin

What do you think?



On Wed, Feb 9, 2011 at 9:39 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:


   The OP's question is easily answered by referring to the
PRODRG FAQ
   in dealing with proper protonation.

   As for Antechamber and the like, these are good tools, but do not
   produce GROMOS-compatible topologies, if that is indeed the
   underlying goal.  We've done thorough analysis of various QM
   calculation methods for GROMOS charges, and none of them produce
   completely satisfactory topologies.  Antechamber, Spartan,
Gaussian,
   etc are good for initial charge calculations, but IMHO do not
   qualify as an "end result" for GROMOS parameterization due to the
   empirical refinement used in the force field derivation.  All of
   that makes GROMOS parameterization somewhat tricky, and hence why
   force field choice is so incredibly important when designing
   projects... ;)

   -Justin


   TJ Mustard wrote:



   Yes I would recommend acpype.

   On February 9, 2011 at 9:42 AM
   jorge_quint...@ciencias.uis.edu.co

   > wrote:

> I think that is better to use antechamber tools.
>
>
> > On 10/02/2011 3:40 AM, mohsen ramezanpour wrote:
> >> Dear Users
> >>
> >> I am using PRODRG to make topology for my drug
> >> It addes Hydrogenes but in wrong way.
> >> My Nitrogen atom is bonded to 2 Carbos,
> >> and PRODRG addes 2 Hydrogenes to it .
> >> Please let me know how can I do.
> >> Thanks in advance
> >
> > This is not really the forum to get help about that. You
   need to read
> > how to PRODRG needs input, and supply something it
can deal
   with. Then
> > do a whole bunch more work testing what it produced.
> >
> > Mark
> > --
> > gmx-users mailing listgmx-users@gromacs.org

   >

> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search
before
   posting!
> > Please don't post (un)subscribe requests to the
list. Use the
> > www interface or send it to
gmx-users-requ...@gromacs.org 
   >.

> > Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
> --
> Jorge R. Quintero
> Químico
> Universidad Industrial 

Re: [gmx-users] Re: Extending the simulation

[Mark Abraham]

On 11/02/2011 8:10 PM, bharat gupta wrote:

Hi,

I extended by 3ns simulation by 2 more ns ... i.e total 5 ns but the 
.xtc file shows only the 3ns trajectories and after checking the 
md.log file , its showing that it completed those 2 ns steps also... 
then how can I get the trajectory for those 2ns ... I used the 
following commands for extending the simulation ...


tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt


I do not understand how the next.log can show "that it completed those 2 
ns steps also".


The old .xtc files will probably have been renamed. Exactly what name 
varies with GROMACS version.


Mark
-- 
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Please search the archive at 
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Re: [gmx-users] PRODRG

[Mark Abraham]

On 11/02/2011 8:18 PM, mohsen ramezanpour wrote:

Dear Dr.Justin

I did it,it works.Thanks.

there are another problem:
I want to add some hydogens to my topology.
I used ADDHYD atomname,But this dosen't work.
PLease let me know how can I include some Hydrogenes in my topology.


As Justin suggested, this is not the right forum for PRODRG advice. This 
forum is for GROMACS discussions. I can only suggest you read the PRODRG 
documentation.


Mark


Thanks in advance
Mohsen

On Thu, Feb 10, 2011 at 7:56 PM, Justin A. Lemkul > wrote:




mohsen ramezanpour wrote:

Dear Dr.Justin

I have read this section before.
There are 2 problem:
1:ADDHYD atomname and DELHYD atomname  commands dosen't work!
they result in ERROR in PRODRG


You have to run PRODRG twice.  The first time, you get the wrong
output.  Note the atom name that PRODRG assigns to your N atom.
 The second time, use DELHYD (name).  If that doesn't work, then I
have no idea and you're better off submitting your question to the
PRODRG developers.


2:Actually I don't know the additional hydrogen is necessary
or not!
Because it may be necessary for proper protonation.
My drug(Sertraline) is in a solvent,it may interact with water
molecules and Nitrogen may  get an additional hydrogen.


A doubly-protonated secondary amine would be a fairly strong acid.
 You should do a pKa calculation to determine what is relevant
rather than guessing.  There are web servers and other software
out there that can do this for you.  Google is your friend.

-Justin

What do you think?



On Wed, Feb 9, 2011 at 9:39 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:


   The OP's question is easily answered by referring to the
PRODRG FAQ
   in dealing with proper protonation.

   As for Antechamber and the like, these are good tools, but
do not
   produce GROMOS-compatible topologies, if that is indeed the
   underlying goal.  We've done thorough analysis of various QM
   calculation methods for GROMOS charges, and none of them
produce
   completely satisfactory topologies.  Antechamber, Spartan,
Gaussian,
   etc are good for initial charge calculations, but IMHO do not
   qualify as an "end result" for GROMOS parameterization due
to the
   empirical refinement used in the force field derivation.
 All of
   that makes GROMOS parameterization somewhat tricky, and
hence why
   force field choice is so incredibly important when designing
   projects... ;)

   -Justin


   TJ Mustard wrote:



   Yes I would recommend acpype.

   On February 9, 2011 at 9:42 AM
jorge_quint...@ciencias.uis.edu.co

> wrote:

> I think that is better to use antechamber tools.
>
>
> > On 10/02/2011 3:40 AM, mohsen ramezanpour wrote:
> >> Dear Users
> >>
> >> I am using PRODRG to make topology for my drug
> >> It addes Hydrogenes but in wrong way.
> >> My Nitrogen atom is bonded to 2 Carbos,
> >> and PRODRG addes 2 Hydrogenes to it .
> >> Please let me know how can I do.
> >> Thanks in advance
> >
> > This is not really the forum to get help about that. You
   need to read
> > how to PRODRG needs input, and supply something it can deal
   with. Then
> > do a whole bunch more work testing what it produced.
> >
> > Mark
> > --
> > gmx-users mailing list gmx-users@gromacs.org

>

> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before
   posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org

>.

> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
> --
> Jorge R. Quintero
> Químico
> Universidad Industrial de Santander
> Bucaramanga, Santander - Colombia
>
> --
> gmx-users mailing list gmx-users@gromacs.org

Re: [gmx-users] Re: crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning (Mark Abraham)

[Mark Abraham]

On 11/02/2011 9:14 PM, Sanjay Kumar Upadhyay wrote:

Sorry, in previous mail i did not write md protocol in details what i
followed for simulation. after energy minimization steps i did PR for 200
ps and then run the production MD. Even i did vacuum energy minimization
before adding solvent for all systems. I used steep followed by cg for
prot-solvent energy minimization which reached up to minimum applied force
100 KJ/mol/nm.


Your results suggest you did not equilibrate well enough. See the link I 
gave last time.


Mark
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Re: [gmx-users] Re: crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning (Mark Abraham)

[Justin A. Lemkul]

Mark Abraham wrote:

On 11/02/2011 9:14 PM, Sanjay Kumar Upadhyay wrote:

Sorry, in previous mail i did not write md protocol in details what i
followed for simulation. after energy minimization steps i did PR for 200
ps and then run the production MD. Even i did vacuum energy minimization
before adding solvent for all systems. I used steep followed by cg for
prot-solvent energy minimization which reached up to minimum applied 
force

100 KJ/mol/nm.


Your results suggest you did not equilibrate well enough. See the link I 
gave last time.




Either that, or incorrect ligand parameters or .mdp settings are being applied, 
breaking the force field model and causing the crash.  Without seeing the .mdp 
and relevant topology(ies), it's impossible to say.


-Justin

--


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


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[gmx-users] Performance in ia64 and x86_64

[Ignacio Fernández Galván]

Hi all,


I'm compiling and testing gromacs 4.5.3 in different machines, and I'm 
wondering 
if it's normal that the ia64 is much slower than the x86_64

I don't know full details of the machines, because I'm not the administrator or 
owner, but /proc/cpuinfo says:

ia64 (128 cores): Dual-Core Intel(R) Itanium(R) Processor 9140N

x86_64 (16 cores): Intel(R) Xeon(R) CPU   E5540  @ 2.53GHz

Just looking at the GHz, one is 2.5 and the other is 1.4, so I'd expect some 
difference, but not a tenfold one: with 8 threads (mdrun -nt 8) I get 0.727 
hours/ns on the x86_64, but 7.607 hours/ns on the ia64. (With 4 threads, it's 
1.3 and 13.7).

I compiled both cases with gcc, although different versions, and default 
options. I had read assembly or fortran kernels could help with ia64, but 
fortran is apparently incompatible with threads, and when I tried with assembly 
the mdrun seemed stuck (no timestep output was written). Is this normal? Is 
there something else I'm missing?

Also, in the x86_64 system I get much lower performance with 12 or 16 threads, 
I 
guess that could be because of the cores/processors, but I don't know what's 
the 
exact configuration of the machine. Again: is this normal?

Thanks,
Ignacio



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[gmx-users] Charges

[Tanos Franca]

Dear gmx users,
Does someone know in which file GROMACS store the information on 
the protein charge. I've seen that after running pdb2gmx or grompp the 
system charge is shown in the screen but we would like to know if this 
information is recorded in some file.

With my best regards,
Tanos C. C. Franca.
Coordinator of the Graduate Program in Chemistry.
Military Institute of Engineering
Rio de Janeiro - RJ
Brazil.
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Re: [gmx-users] Re: Extending the simulation

[bharat gupta]

Ya I found that the new trajectory is saved with name traj.trr and traj.xtc
... and I remember I saved the new tpr file as next.tpr..

Now I want to merge the two trajectories and the two .tpr files... I found
trjcat can be used ... I used the following command: -

trjcat -f1 md_0_1.xtc -f2 traj.xtc -o trjout.xtc

but its giving error ..

Can u tell me how to merge both the .tpr and .xtc files

On Fri, Feb 11, 2011 at 3:34 AM, Mark Abraham wrote:

>  On 11/02/2011 8:10 PM, bharat gupta wrote:
>
> Hi,
>
>  I extended by 3ns simulation by 2 more ns ... i.e total 5 ns but the .xtc
> file shows only the 3ns trajectories and after checking the md.log file ,
> its showing that it completed those 2 ns steps also... then how can I get
> the trajectory for those 2ns ... I used the following commands for extending
> the simulation ...
>
>  tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
> mdrun -s next.tpr -cpi previous.cpt
>
>
> I do not understand how the next.log can show "that it completed those 2 ns
> steps also".
>
> The old .xtc files will probably have been renamed. Exactly what name
> varies with GROMACS version.
>
> Mark
>
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Re: [gmx-users] Charges

[Justin A. Lemkul]

Tanos Franca wrote:

Dear gmx users,
Does someone know in which file GROMACS store the information on the 
protein charge. I've seen that after running pdb2gmx or grompp the 
system charge is shown in the screen but we would like to know if this 
information is recorded in some file.


It's in your topology.  The "qtot" entry keeps a running total of the charge on 
the protein.  The last line in [atoms] indicates the overall net charge.


-Justin


With my best regards,
Tanos C. C. Franca.
Coordinator of the Graduate Program in Chemistry.
Military Institute of Engineering
Rio de Janeiro - RJ
Brazil.


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MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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Re: [gmx-users] Re: Extending the simulation

[Justin A. Lemkul]

bharat gupta wrote:
Ya I found that the new trajectory is saved with name traj.trr and 
traj.xtc ... and I remember I saved the new tpr file as next.tpr..


Now I want to merge the two trajectories and the two .tpr files... I 
found trjcat can be used ... I used the following command: -


trjcat -f1 md_0_1.xtc -f2 traj.xtc -o trjout.xtc

but its giving error ..



You're not supplying valid command line flags; -f1 and -f2 don't exist.  See 
trjcat -h.



Can u tell me how to merge both the .tpr and .xtc files



There is no need to merge .tpr files, nor can they be.

-Justin

On Fri, Feb 11, 2011 at 3:34 AM, Mark Abraham > wrote:


On 11/02/2011 8:10 PM, bharat gupta wrote:

Hi,

I extended by 3ns simulation by 2 more ns ... i.e total 5 ns but
the .xtc file shows only the 3ns trajectories and after checking
the md.log file , its showing that it completed those 2 ns steps
also... then how can I get the trajectory for those 2ns ... I used
the following commands for extending the simulation ...

tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt


I do not understand how the next.log can show "that it completed
those 2 ns steps also".

The old .xtc files will probably have been renamed. Exactly what
name varies with GROMACS version.

Mark

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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



--


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


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[gmx-users] NVT run

[Thomas Koller]

Hello,

I calculate the density of my lquid in the equilibrated time range of the 
density-time plots (NPT runs). I use the gro file of these NPT runs for NVT 
runs to calculate the self diffusion coefficient at the simulated density. 
Concerning this gro file: Is this taken from the end of the NPT run or the 
average of the equilibrated time range? Because this is important for the 
following NVT simulation. Which system size is listed there at the bottom of 
the output gro file?

Regards,
Thomas
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Re: [gmx-users] NVT run

[Mark Abraham]

On 12/02/2011 12:02 AM, Thomas Koller wrote:

Hello,

I calculate the density of my lquid in the equilibrated time range of the 
density-time plots (NPT runs). I use the gro file of these NPT runs for NVT 
runs to calculate the self diffusion coefficient at the simulated density. 
Concerning this gro file: Is this taken from the end of the NPT run or the 
average of the equilibrated time range? Because this is important for the 
following NVT simulation. Which system size is listed there at the bottom of 
the output gro file?


The file written by mdrun -c is the simulation end point.

Mark
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Re: [gmx-users] NVT run

[Justin A. Lemkul]

Thomas Koller wrote:

Hello,

I calculate the density of my lquid in the equilibrated time range of the
density-time plots (NPT runs). I use the gro file of these NPT runs for NVT
runs to calculate the self diffusion coefficient at the simulated density.
Concerning this gro file: Is this taken from the end of the NPT run or the
average of the equilibrated time range? Because this is important for the


mdrun -h:

..."The structure file (-c) contains the coordinates and velocities of the last 
step."...



following NVT simulation. Which system size is listed there at the bottom of
the output gro file?



The one corresponding to that configuration, i.e. the last step.

-Justin


Regards, Thomas


--


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


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Re: [gmx-users] Performance in ia64 and x86_64

[Mark Abraham]

On 11/02/2011 11:33 PM, Ignacio Fernández Galván wrote:

Hi all,


I'm compiling and testing gromacs 4.5.3 in different machines, and I'm wondering
if it's normal that the ia64 is much slower than the x86_64

I don't know full details of the machines, because I'm not the administrator or
owner, but /proc/cpuinfo says:

ia64 (128 cores): Dual-Core Intel(R) Itanium(R) Processor 9140N

x86_64 (16 cores): Intel(R) Xeon(R) CPU   E5540  @ 2.53GHz

Just looking at the GHz, one is 2.5 and the other is 1.4, so I'd expect some
difference, but not a tenfold one: with 8 threads (mdrun -nt 8) I get 0.727
hours/ns on the x86_64, but 7.607 hours/ns on the ia64. (With 4 threads, it's
1.3 and 13.7).

I compiled both cases with gcc, although different versions, and default
options. I had read assembly or fortran kernels could help with ia64, but
fortran is apparently incompatible with threads, and when I tried with assembly
the mdrun seemed stuck (no timestep output was written). Is this normal? Is
there something else I'm missing?


GROMACS assembly kernels for IA64 have been known to have problems (see 
mailing list archives), but IIRC usually in compilation, not execution. 
You will need to inspect the first few hundred lines of the .log files 
where GROMACS reports what kernels are being used for the execution.



Also, in the x86_64 system I get much lower performance with 12 or 16 threads, I
guess that could be because of the cores/processors, but I don't know what's the
exact configuration of the machine. Again: is this normal?


We can't say with the information given. For best performance, the 
number of threads cannot exceed the number of physical cores available 
to one processor. To go higher, you need to compile and use GROMACS with 
MPI, not threading. If the IA64 is "dual core" then you are not 
measuring anything useful. You also need to be sure you're measuring for 
a decent length of time - a few minutes at least.


Mark
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Re: [gmx-users] Fwd: Question on Gromacs: rlist, rvdw, rcoulomb

[Mark Abraham]

I am a user of gromacs. I am quite confused when I came across the
relation of rlist and rvdw / rcoulomb in vdw and coulomb calculation.

In cut-off, it says rvdw / rcoulomb should be greater than rlist, while
in switch/shift, it says rvdw should be smaller than rlist...

I guess in cut-off, it's to get all the updated atoms in the calculation
of vdw/ coulomb by setting rvdw/ rcoulomb greater, but why it's the
opposite in switch...

Could you help me to understand how it's done? Thanks a lot. 


They're different algorithms, and they work as described. rlist controls 
the size of the neighbour lists, which list all the atom pairs whose 
interactions the nonbonded kernels compute each MD step. rvdw/rcoulomb 
control where the interaction is judged to be small enough that 
particles at greater distances can be neglected. The only basis 
governing their relative size is the algorithm you want to implement. 
With twin-range neighbourlists, the interactions between rvdw and 
rcoulomb and rlist are computed whenever the neighbour lists are 
constructed, and re-used for nstlist steps (see manual 3.4.2). With 
switch/shift interactions, GROMACS generates the potential in tabular 
form, so that if rlist > rvdw, then some interactions will be computed 
at distances such that the resulting potential will be known to be zero 
(see manual 4.1.5). In both cases there's a trade-off between the cost 
of re-constructing the neighbour lists, the cost of evaluating the 
resulting interactions and the accuracy limitations imposed by the 
underlying assumptions.


Mark
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Re: [gmx-users] Fwd: Question on Gromacs: rlist, rvdw, rcoulomb

[Erik Marklund]

Mark Abraham skrev 2011-02-11 14.17:

I am a user of gromacs. I am quite confused when I came across the
relation of rlist and rvdw / rcoulomb in vdw and coulomb calculation.

In cut-off, it says rvdw / rcoulomb should be greater than rlist, while
in switch/shift, it says rvdw should be smaller than rlist...

I guess in cut-off, it's to get all the updated atoms in the calculation
of vdw/ coulomb by setting rvdw/ rcoulomb greater, but why it's the
opposite in switch...

Could you help me to understand how it's done? Thanks a lot. 


They're different algorithms, and they work as described. rlist 
controls the size of the neighbour lists, which list all the atom 
pairs whose interactions the nonbonded kernels compute each MD step. 
rvdw/rcoulomb control where the interaction is judged to be small 
enough that particles at greater distances can be neglected. The only 
basis governing their relative size is the algorithm you want to 
implement. With twin-range neighbourlists, the interactions between 
rvdw and rcoulomb and rlist are computed whenever the neighbour lists 
are constructed, and re-used for nstlist steps (see manual 3.4.2). 
With switch/shift interactions, GROMACS generates the potential in 
tabular form, so that if rlist > rvdw, then some interactions will be 
computed at distances such that the resulting potential will be known 
to be zero (see manual 4.1.5). In both cases there's a trade-off 
between the cost of re-constructing the neighbour lists, the cost of 
evaluating the resulting interactions and the accuracy limitations 
imposed by the underlying assumptions.


Mark
And if I'm not mistaken (if I am, please do correct me) the reason for 
having rlist > rvdw with shift/switch is that the neighbourlists are 
made based on charge group distance rather than atomic distances. Hence 
there may be atoms closer than rvdw in the neighbourlists although the 
centers of their respective chargegroups are separated by more than rvdw.


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Re: [gmx-users] Performance in ia64 and x86_64

[Ignacio Fernández Galván]

 Original Message 
From: Mark Abraham 

> We can't say with the information given. For best performance, the number of
> threads cannot exceed the number of physical cores available to one processor.
> To go higher, you need to compile and use GROMACS with MPI, not threading. If
> the IA64 is "dual core" then you are not measuring anything useful. You also 
>need
> to be sure you're measuring for a decent length of time - a few minutes at 
>least.


It seems the x86_64 processor has 4 cores and 8 threads support 
(), so the machine has probably two 
physical processors. I thought MPI was only needed if there was network 
communication involved, as in a cluster, but not in SMP, which is what both 
machines are (single memory, single OS), I guess I was wrong. I'll try 
compiling 
with MPI.

Thanks,
Ignacio



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Re: [gmx-users] Performance in ia64 and x86_64

[Carsten Kutzner]

Hi Ignacio,

On Feb 11, 2011, at 1:33 PM, Ignacio Fernández Galván wrote:

> Hi all,
> 
> 
> I'm compiling and testing gromacs 4.5.3 in different machines, and I'm 
> wondering 
> if it's normal that the ia64 is much slower than the x86_64
> 
> I don't know full details of the machines, because I'm not the administrator 
> or 
> owner, but /proc/cpuinfo says:
> 
> ia64 (128 cores): Dual-Core Intel(R) Itanium(R) Processor 9140N
> 
> x86_64 (16 cores): Intel(R) Xeon(R) CPU   E5540  @ 2.53GHz
> 
> Just looking at the GHz, one is 2.5 and the other is 1.4, so I'd expect some 
> difference, but not a tenfold one: with 8 threads (mdrun -nt 8) I get 0.727 
> hours/ns on the x86_64, but 7.607 hours/ns on the ia64. (With 4 threads, it's 
> 1.3 and 13.7).
> 
> I compiled both cases with gcc, although different versions, and default 
> options. I had read assembly or fortran kernels could help with ia64, but 
> fortran is apparently incompatible with threads, and when I tried with 
> assembly 
> the mdrun seemed stuck (no timestep output was written). Is this normal? Is 
Yes, there is a problem with the ia64 assembly loops and this is exactly
how it manifests. I did run into that problem several times. What you can
do is to use the fortran kernels and compile with MPI. The performance
of the threaded and MPI versions should be the same, and the fortran 
kernels are nearly as fast as the ia64 assembly. Probably you can speed
things up a few percent by using the Intel compiler.

Cheers,
  Carsten



> there something else I'm missing?
> 
> Also, in the x86_64 system I get much lower performance with 12 or 16 
> threads, I 
> guess that could be because of the cores/processors, but I don't know what's 
> the 
> exact configuration of the machine. Again: is this normal?
> 
> Thanks,
> Ignacio
> 
> 
> 
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[gmx-users] extracting a structure from confout.gro file

[najwa drici]

hi all


I would like to extract my protein structure with the first
hydration shell around the active site which contains an ion from counfout.gro.

Is there any program script able to do this?

Cordially DRICI nedjoua


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Re: [gmx-users] extracting a structure from confout.gro file

[Justin A. Lemkul]

najwa drici wrote:

hi all

I would like to extract my protein structure with the first hydration 
shell around the active site which contains an ion from counfout.gro.


Is there any program script able to do this?



Not in one step, no.  You could:

1. Use make_ndx to create an index group that defines your active site.

2. Use g_dist -dist to determine which water molecules (based on the atoms 
listed) are within a defined distance from the active site residues.


3. Make another index group that contains protein + the waters identified in 
step 2.

4. Extract those coordinates using trjconv and the index group created in step 
3.

-Justin


Cordially DRICI nedjoua




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


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[gmx-users] rotamers and rings

[abdullah ahmed]

Hello gromacs users, I have asked this question before but perhaps I was not 
clear enough. I noticed that in Gromacs verisons 4.5.3 and 3.3.4 when the 
initial structure has some side chains located very close to each other then 
after energy minimisation they become distorted (for example, Phe ring is not 
flat, and for Leu some hydrogen atoms move away from the rest of the side 
chain).I realize that these problems are probably due very close packing of the 
sidechains in the initial structure. But I hope to keep the close contacts in 
the initial structure and obtain correct stereochemistry of the molecule after 
the minimisation. Is this possible? Sorry for bothering you again and thank you 
in advance for your help,Abdullah Ahmed 
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Re: [gmx-users] rotamers and rings

[Justin A. Lemkul]

abdullah ahmed wrote:

Hello gromacs users,

I have asked this question before but perhaps I was not clear enough. I
noticed that in Gromacs verisons 4.5.3 and 3.3.4 when the initial structure
has some side chains located very close to each other then after energy
minimisation they become distorted (for example, Phe ring is not flat, and
for Leu some hydrogen atoms move away from the rest of the side chain).

I realize that these problems are probably due very close packing of the
sidechains in the initial structure.

But I hope to keep the close contacts in the initial structure and obtain
correct stereochemistry of the molecule after the minimisation. Is this
possible?



The outcome of energy minimization is dictated by the functional form of your 
chosen force field and the parameters it assigns to the constituent atoms in 
your structure.  If you're getting unreasonable geometry after EM, then your 
starting structure is physically unreasonable.  You could try to restrain and/or 
freeze these configurations, but I would suspect that any subsequent MD will 
crash instantly when these atoms shear apart from one another.  If the 
configuration is not stable in EM, it will not be stable in MD.


-Justin


Sorry for bothering you again and thank you in advance for your help,

Abdullah Ahmed



--


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


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[gmx-users] only one model is displayed

[Kwee Hong]

Hi,

I've used g_confrms from gromacs-4.5.1 to compare two structures with the 
following command line -

   g_confrms -f1 1OMB.pdb -f2 md.gro -o fit.pdb

fit.pdb  is supposed to be the output file which would show the 2 structures 
superimposed on  each other. But when I visualised it with vmd. I can only see 
one  structure.

Any idea what's going on? I hereby attached part of the generated fit.pdb.

All suggestions are welcomed.

Regards,
Joyce


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[gmx-users] Re: only one model is displayed

[Kwee Hong]

sorry, forgot to attached the file...





From: Kwee Hong 
To: gmx-users 
Sent: Friday, February 11, 2011 23:38:55
Subject: only one model is displayed


Hi,

I've used g_confrms from gromacs-4.5.1 to compare two structures with the 
following command line -

   g_confrms -f1 1OMB.pdb -f2 md.gro -o fit.pdb

fit.pdb  is supposed to be the output file which would show the 2 structures 
superimposed on  each other. But when I visualised it with vmd. I can only see 
one  structure.

Any idea what's going on? I hereby attached part of the generated fit.pdb.

All suggestions are welcomed.

Regards,
Joyce



fit.pdb
Description: Binary data
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Re: [gmx-users] Re: only one model is displayed

[Justin A. Lemkul]

There are two models.  VMD loads them as sequential frames such that they can be 
animated.  You'll see frame "0" and "1" in the VMD main window.


-Justin

Kwee Hong wrote:

sorry, forgot to attached the file...


*From:* Kwee Hong 
*To:* gmx-users 
*Sent:* Friday, February 11, 2011 23:38:55
*Subject:* only one model is displayed

Hi,

I've used g_confrms from gromacs-4.5.1 to compare two structures with 
the following command line -


   g_confrms -f1 1OMB.pdb -f2 md.gro -o fit.pdb

fit.pdb is supposed to be the output file which would show the 2 
structures superimposed on each other. But when I visualised it with 
vmd. I can only see one structure.


Any idea what's going on? I hereby attached part of the generated fit.pdb.

All suggestions are welcomed.

Regards,
Joyce




--


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


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Re: [gmx-users] doubts on g_confrms output

[Kwee Hong]

Hi Tsjerk,

Thanks for the help. I got it.
But do you have any idea how to solve this in vmd?

Regards,
Joyce





From: Tsjerk Wassenaar 
To: Discussion list for GROMACS users 
Sent: Saturday, January 22, 2011 15:53:22
Subject: Re: [gmx-users] doubts on g_confrms output


Hi Joyce,
In pymol use 'set all_states'
Cheers,
Tsjerk
On Jan 22, 2011 8:30 AM, "Kwee Hong"  wrote:
>
>
>Hi,
>
>
>I was trying to do some analysis following John's "GROMACS tutorial for 
>solvation study of spider toxin peptide".
>I'm using GROMACS-4.5.3 and my command line for g_confrms is 
>
>
>g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb
>
>
>The program calculated the RMSD sucessfully and fit_wet.pdb was generated. 
>Yet, 
>when i tried to visualise fit_wet.pdb using VMD, the structure is obviously in 
>a 
>mess. And when I tried it out  with pymol, I can only visualised one model. 
>Model 2 did not appear. I wonder would it be the pdb format generated by 
>g_confrms is not the standard pdb format and had caused VMD and final failed 
>to 
>read  them?
>
>
>Herein, I attached part of the pdb file generated by  fit_wet.pdb. Any insight 
>is welcomed.
>
>
>Thanks,
>Joyce
>
>
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>http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] doubts on g_confrms output

[Mark Abraham]

On 12/02/2011 2:55 AM, Kwee Hong wrote:

Hi Tsjerk,

Thanks for the help. I got it.
But do you have any idea how to solve this in vmd?


Use trjconv -sep on the .pdb file to split it.

Mark



Regards,
Joyce


*From:* Tsjerk Wassenaar 
*To:* Discussion list for GROMACS users 
*Sent:* Saturday, January 22, 2011 15:53:22
*Subject:* Re: [gmx-users] doubts on g_confrms output

Hi Joyce,

In pymol use 'set all_states'

Cheers,

Tsjerk

On Jan 22, 2011 8:30 AM, "Kwee Hong" > wrote:


Hi,

I was trying to do some analysis following John's "GROMACS tutorial 
for solvation study of spider toxin peptide".

I'm using GROMACS-4.5.3 and my command line for g_confrms is

g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb

The program calculated the RMSD sucessfully and fit_wet.pdb was 
generated. Yet, when i tried to visualise fit_wet.pdb using VMD, the 
structure is obviously in a mess. And when I tried it out with pymol, 
I can only visualised one model. Model 2 did not appear. I wonder 
would it be the pdb format generated by g_confrms is not the standard 
pdb format and had caused VMD and final failed to read them?


Herein, I attached part of the pdb file generated by fit_wet.pdb. Any 
insight is welcomed.


Thanks,
Joyce



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Re: [gmx-users] extracting a structure from confout.gro file

[Mark Abraham]

On 12/02/2011 1:51 AM, Justin A. Lemkul wrote:



najwa drici wrote:

hi all

I would like to extract my protein structure with the first hydration 
shell around the active site which contains an ion from counfout.gro.


Is there any program script able to do this?



Not in one step, no.  You could:

1. Use make_ndx to create an index group that defines your active site.

2. Use g_dist -dist to determine which water molecules (based on the 
atoms listed) are within a defined distance from the active site 
residues.


3. Make another index group that contains protein + the waters 
identified in step 2.


Or g_select to do some/all of 1-3.

Mark

4. Extract those coordinates using trjconv and the index group created 
in step 3.


-Justin


Cordially DRICI nedjoua






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[gmx-users] Add custom residue to DNA index group

[william Stebbeds]

Hi Folks,

I have added a custom DNA residue to the amber99sb ff, and everything works 
perfectly, (thanks to Justin!).

The residue is incorporated perfectly into the sequence, with no abnormal 
events during simulations. I have updated all the files to include the new 
residue.

I have since realised, when using g_rms, that my custom residue is not included 
in the default DNA index group, and appears as a group on its own.

Is  there a way of making gromacs understand that this residue is DNA when it 
makes the index files?

I am not using make_ndx, I just let gromacs split the groups.

Thanks in advance

Will - Cranfield University
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Re: [gmx-users] Performance in ia64 and x86_64

[Mark Abraham]

On 12/02/2011 12:44 AM, Ignacio Fernández Galván wrote:

 Original Message 
From: Mark Abraham


We can't say with the information given. For best performance, the number of
threads cannot exceed the number of physical cores available to one processor.
To go higher, you need to compile and use GROMACS with MPI, not threading. If
the IA64 is "dual core" then you are not measuring anything useful. You also
need
to be sure you're measuring for a decent length of time - a few minutes at
least.


It seems the x86_64 processor has 4 cores and 8 threads support
(), so the machine has probably two
physical processors.


That's delivered via hyper-threading (see bottom of that page). GROMACS 
is unlikely to get any significant value out of that, because the 
number-crunching loops of the code dominate the execution time, and by 
design GROMACS doesn't do many cache misses, branch mispredictions, etc. 
in those loops, so the second thread doesn't have much dead time to use. 
HT is good for desktop workstations that can expect to do lots of that 
kind of thing. Secondarily, it probably doubles the pressure on the 
cache (but MD is normally fairly cache-friendly).



  I thought MPI was only needed if there was network
communication involved, as in a cluster, but not in SMP, which is what both
machines are (single memory, single OS), I guess I was wrong. I'll try compiling
with MPI.


As I understand it, useful threading has got to do with how many cores 
are on the same piece of processor silicon, not whether the memory is 
shared between processors. Xeon E5540 has 4 physical cores per 
processor, so that's as far as GROMACS will usefully thread. The good 
news is that if you really have shared memory, that does make 
MPI-GROMACS almost indistinguishably fast from a threaded version 
running on the theoretically equivalent hardware. I have a vaguely 
similar machine, but with dual quad-core Xeon X5570 processors. MPI and 
threading work indistinguishably out to 8 processes, then threading stops.


Mark
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Re: [gmx-users] Add custom residue to DNA index group

[Mark Abraham]

On 12/02/2011 3:14 AM, william Stebbeds wrote:

Hi Folks,

I have added a custom DNA residue to the amber99sb ff, and everything 
works perfectly, (thanks to Justin!).


The residue is incorporated perfectly into the sequence, with no 
abnormal events during simulations. I have updated all the files to 
include the new residue.


I have since realised, when using g_rms, that my custom residue is not 
included in the default DNA index group, and appears as a group on its 
own.


Is  there a way of making gromacs understand that this residue is DNA 
when it makes the index files?


I am not using make_ndx, I just let gromacs split the groups.

Thanks in advance

Will - Cranfield University


You need to arrange for the tools to access a modified form of 
share/gromacs/top/residuetypes.dat with your custom residue suitably 
classified. I understand you can copy that file to your working 
directory and modify it there, and GROMACS will use the local copy.


Mark
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RE: [gmx-users] Add custom residue to DNA index group

[william Stebbeds]

Thanks for the quick reply, 

I have already done that, and GROMACS, in all other cases, knows it is DNA, as 
it automatically forms the bonds with other residues.

it is only when it makes its index files that it doesnt know that my residue is 
DNA.

Cheers

Will

 




Date: Sat, 12 Feb 2011 03:33:15 +1100
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Add custom residue to DNA index group



  



Message body
  
  
On 12/02/2011 3:14 AM, william Stebbeds wrote:

  
  Hi Folks,

  

  I have added a custom DNA residue to the amber99sb ff, and
  everything works perfectly, (thanks to Justin!).

  

  The residue is incorporated perfectly into the sequence, with no
  abnormal events during simulations. I have updated all the files
  to include the new residue.

  

  I have since realised, when using g_rms, that my custom residue is
  not included in the default DNA index group, and appears as a
  group on its own.

  

  Is  there a way of making gromacs understand that this residue is
  DNA when it makes the index files?

  

  I am not using make_ndx, I just let gromacs split the groups.

  

  Thanks in advance

  

  Will - Cranfield University




You need to arrange for the tools to access a modified form of
share/gromacs/top/residuetypes.dat with your custom residue suitably
classified. I understand you can copy that file to your working
directory and modify it there, and GROMACS will use the local copy.



Mark

  


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Re: [gmx-users] doubts on g_confrms output

[Kwee Hong]

Hi Mark,

I tried but with this error:

Fatal error:
Number of atoms in pdb frame 0 is 331 instead of 491

Joyce





From: Mark Abraham 
To: Discussion list for GROMACS users 
Sent: Saturday, February 12, 2011 0:01:39
Subject: Re: [gmx-users] doubts on g_confrms output

On 12/02/2011 2:55 AM, Kwee Hong wrote: 
Hi Tsjerk,
>
>Thanks for the help. I got it.
>But do you have any idea how to solve this in vmd?
>
Use trjconv -sep on the .pdb file to split it.

Mark



>Regards,
>Joyce
>
>
>
>

From: Tsjerk Wassenaar 
>To: Discussion list for GROMACS users 
>Sent: Saturday, January 22, 2011 15:53:22
>Subject: Re: [gmx-users] doubts on g_confrms output
>
>
>Hi Joyce,
>In pymol use 'set all_states'
>Cheers,
>Tsjerk
>On Jan 22, 2011 8:30 AM, "Kwee Hong" 
> 
>wrote:
>>
>>
>>Hi,
>>
>>
>>I was trying to do some analysis following John's 
>>"GROMACS tutorial for solvation study of spider 
>>toxin peptide".
>>I'm using GROMACS-4.5.3 and my command line for 
>>g_confrms is 
>>
>>
>>g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb
>>
>>
>>The program calculated the RMSD sucessfully and 
>>fit_wet.pdb was generated. Yet, when i tried to 
>>visualise fit_wet.pdb using VMD, the structure is 
>>obviously in a mess. And when I tried it out with 
>>pymol, I can only visualised one model. Model 2 
>>did 
>>not appear. I wonder would it be the pdb format 
>>generated by g_confrms is not the standard pdb 
>>format and had caused VMD and final failed to 
>>read 
>>them?
>>
>>
>>Herein, I attached part of the pdb file generated 
>>by 
>>fit_wet.pdb. Any insight is welcomed.
>>
>>
>>Thanks,
>>Joyce
>>
>>
>>--
>>gmx-users mailing listgmx-users@gromacs.org
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at 
>>http://www.gromacs.org/Support/Mailing_Lists/Search 
>>before posting!
>>Please don't post (un)subscribe requests to the list. Use   the
>>www interface or send it to gmx-users-requ...@gromacs.org.
>>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>


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RE: [gmx-users] Add custom residue to DNA index group

[Sarath Chandra Dantu]

>
> Thanks for the quick reply,
>
> I have already done that, and GROMACS, in all other cases, knows it is
> DNA, as it automatically forms the bonds with other residues.
>
> it is only when it makes its index files that it doesnt know that my
> residue is DNA.
>

Did you make the change in residuetypes.dat file.
add your residues XXX as DNA in the residuetypes.dat file

eq: XXX  DNA



Best Wishes,

Sarath
> Cheers
>
> Will
>
>
>
>
>
>
> Date: Sat, 12 Feb 2011 03:33:15 +1100
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Add custom residue to DNA index group
>
>
>
>
>
>
>
> Message body
>
>
> On 12/02/2011 3:14 AM, william Stebbeds wrote:
>
>
>   Hi Folks,
>
>
>
>   I have added a custom DNA residue to the amber99sb ff, and
>   everything works perfectly, (thanks to Justin!).
>
>
>
>   The residue is incorporated perfectly into the sequence, with no
>   abnormal events during simulations. I have updated all the files
>   to include the new residue.
>
>
>
>   I have since realised, when using g_rms, that my custom residue is
>   not included in the default DNA index group, and appears as a
>   group on its own.
>
>
>
>   Is  there a way of making gromacs understand that this residue is
>   DNA when it makes the index files?
>
>
>
>   I am not using make_ndx, I just let gromacs split the groups.
>
>
>
>   Thanks in advance
>
>
>
>   Will - Cranfield University
>
>
>
>
> You need to arrange for the tools to access a modified form of
> share/gromacs/top/residuetypes.dat with your custom residue suitably
> classified. I understand you can copy that file to your working
> directory and modify it there, and GROMACS will use the local copy.
>
>
>
> Mark
>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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RE: [gmx-users] Add custom residue to DNA index group

[william Stebbeds]

Indeed I did

DGO  DNA

Cheers

Will

> Date: Fri, 11 Feb 2011 17:57:32 +0100
> Subject: RE: [gmx-users] Add custom residue to DNA index group
> From: dsar...@gwdg.de
> To: gmx-users@gromacs.org
> 
> >
> > Thanks for the quick reply,
> >
> > I have already done that, and GROMACS, in all other cases, knows it is
> > DNA, as it automatically forms the bonds with other residues.
> >
> > it is only when it makes its index files that it doesnt know that my
> > residue is DNA.
> >
> 
> Did you make the change in residuetypes.dat file.
> add your residues XXX as DNA in the residuetypes.dat file
> 
> eq: XXX  DNA
> 
> 
> 
> Best Wishes,
> 
> Sarath
> > Cheers
> >
> > Will
> >
> >
> >
> >
> >
> >
> > Date: Sat, 12 Feb 2011 03:33:15 +1100
> > From: mark.abra...@anu.edu.au
> > To: gmx-users@gromacs.org
> > Subject: Re: [gmx-users] Add custom residue to DNA index group
> >
> >
> >
> >
> >
> >
> >
> > Message body
> >
> >
> > On 12/02/2011 3:14 AM, william Stebbeds wrote:
> >
> >
> >   Hi Folks,
> >
> >
> >
> >   I have added a custom DNA residue to the amber99sb ff, and
> >   everything works perfectly, (thanks to Justin!).
> >
> >
> >
> >   The residue is incorporated perfectly into the sequence, with no
> >   abnormal events during simulations. I have updated all the files
> >   to include the new residue.
> >
> >
> >
> >   I have since realised, when using g_rms, that my custom residue is
> >   not included in the default DNA index group, and appears as a
> >   group on its own.
> >
> >
> >
> >   Is  there a way of making gromacs understand that this residue is
> >   DNA when it makes the index files?
> >
> >
> >
> >   I am not using make_ndx, I just let gromacs split the groups.
> >
> >
> >
> >   Thanks in advance
> >
> >
> >
> >   Will - Cranfield University
> >
> >
> >
> >
> > You need to arrange for the tools to access a modified form of
> > share/gromacs/top/residuetypes.dat with your custom residue suitably
> > classified. I understand you can copy that file to your working
> > directory and modify it there, and GROMACS will use the local copy.
> >
> >
> >
> > Mark
> >
> >
> >
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [gmx-users] Add custom residue to DNA index group

[Justin A. Lemkul]

william Stebbeds wrote:

Indeed I did

DGO  DNA



Did you make the change system-wide, or in a local directory?  If the latter, 
you have to issue all your commands in that same directory or else the default 
residuetypes.dat (in GMXLIB) will be read.


Can you post the make_ndx output (i.e. list of groups)?

-Justin


Cheers

Will

 > Date: Fri, 11 Feb 2011 17:57:32 +0100
 > Subject: RE: [gmx-users] Add custom residue to DNA index group
 > From: dsar...@gwdg.de
 > To: gmx-users@gromacs.org
 >
 > >
 > > Thanks for the quick reply,
 > >
 > > I have already done that, and GROMACS, in all other cases, knows it is
 > > DNA, as it automatically forms the bonds with other residues.
 > >
 > > it is only when it makes its index files that it doesnt know that my
 > > residue is DNA.
 > >
 >
 > Did you make the change in residuetypes.dat file.
 > add your residues XXX as DNA in the residuetypes.dat file
 >
 > eq: XXX DNA
 >
 >
 >
 > Best Wishes,
 >
 > Sarath
 > > Cheers
 > >
 > > Will
 > >
 > >
 > >
 > >
 > >
 > >
 > > Date: Sat, 12 Feb 2011 03:33:15 +1100
 > > From: mark.abra...@anu.edu.au
 > > To: gmx-users@gromacs.org
 > > Subject: Re: [gmx-users] Add custom residue to DNA index group
 > >
 > >
 > >
 > >
 > >
 > >
 > >
 > > Message body
 > >
 > >
 > > On 12/02/2011 3:14 AM, william Stebbeds wrote:
 > >
 > >
 > > Hi Folks,
 > >
 > >
 > >
 > > I have added a custom DNA residue to the amber99sb ff, and
 > > everything works perfectly, (thanks to Justin!).
 > >
 > >
 > >
 > > The residue is incorporated perfectly into the sequence, with no
 > > abnormal events during simulations. I have updated all the files
 > > to include the new residue.
 > >
 > >
 > >
 > > I have since realised, when using g_rms, that my custom residue is
 > > not included in the default DNA index group, and appears as a
 > > group on its own.
 > >
 > >
 > >
 > > Is there a way of making gromacs understand that this residue is
 > > DNA when it makes the index files?
 > >
 > >
 > >
 > > I am not using make_ndx, I just let gromacs split the groups.
 > >
 > >
 > >
 > > Thanks in advance
 > >
 > >
 > >
 > > Will - Cranfield University
 > >
 > >
 > >
 > >
 > > You need to arrange for the tools to access a modified form of
 > > share/gromacs/top/residuetypes.dat with your custom residue suitably
 > > classified. I understand you can copy that file to your working
 > > directory and modify it there, and GROMACS will use the local copy.
 > >
 > >
 > >
 > > Mark
 > >
 > >
 > >
 > >
 > > --
 > > gmx-users mailing list gmx-users@gromacs.org
 > > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > > Please search the archive at
 > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 > > Please don't post (un)subscribe requests to the list. Use the
 > > www interface or send it to gmx-users-requ...@gromacs.org.
 > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 > > --
 > > gmx-users mailing list gmx-users@gromacs.org
 > > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > > Please search the archive at
 > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 > > Please don't post (un)subscribe requests to the list. Use the
 > > www interface or send it to gmx-users-requ...@gromacs.org.
 > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 >
 >
 >
 > --
 > gmx-users mailing list gmx-users@gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!

 > Please don't post (un)subscribe requests to the list. Use the
 > www interface or send it to gmx-users-requ...@gromacs.org.
 > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



--


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


--
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Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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RE: [gmx-users] Add custom residue to DNA index group

[william Stebbeds]

I made the changes to ../gromacs/top/residuetypes.dat

the Make_ndx output:

  0 System  : 34023 atoms
  1 DNA :   650 atoms
  2 DGO :66 atoms
  3 K   :43 atoms
  4 CL  :21 atoms
  5 Other   :66 atoms
  6 DGO :66 atoms
  7 K   :43 atoms
  8 CL  :21 atoms
  9 Ion :64 atoms
 10 DGO :66 atoms
 11 K   :43 atoms
 12 CL  :21 atoms
 13 Water   : 33243 atoms
 14 SOL : 33243 atoms
 15 non-Water   :   780 atoms
 16 Water_and_ions  : 33307 atoms

This system consists of a 22 residue DNA molecule, two of which are DGO, each 
have 33 atoms.

I also do not understand why DGO is repeated three times.

Thanks again

will


> Date: Fri, 11 Feb 2011 12:08:52 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Add custom residue to DNA index group
> 
> 
> 
> william Stebbeds wrote:
> > Indeed I did
> > 
> > DGO  DNA
> > 
> 
> Did you make the change system-wide, or in a local directory?  If the latter, 
> you have to issue all your commands in that same directory or else the 
> default 
> residuetypes.dat (in GMXLIB) will be read.
> 
> Can you post the make_ndx output (i.e. list of groups)?
> 
> -Justin
> 
> > Cheers
> > 
> > Will
> > 
> >  > Date: Fri, 11 Feb 2011 17:57:32 +0100
> >  > Subject: RE: [gmx-users] Add custom residue to DNA index group
> >  > From: dsar...@gwdg.de
> >  > To: gmx-users@gromacs.org
> >  >
> >  > >
> >  > > Thanks for the quick reply,
> >  > >
> >  > > I have already done that, and GROMACS, in all other cases, knows it is
> >  > > DNA, as it automatically forms the bonds with other residues.
> >  > >
> >  > > it is only when it makes its index files that it doesnt know that my
> >  > > residue is DNA.
> >  > >
> >  >
> >  > Did you make the change in residuetypes.dat file.
> >  > add your residues XXX as DNA in the residuetypes.dat file
> >  >
> >  > eq: XXX DNA
> >  >
> >  >
> >  >
> >  > Best Wishes,
> >  >
> >  > Sarath
> >  > > Cheers
> >  > >
> >  > > Will
> >  > >
> >  > >
> >  > >
> >  > >
> >  > >
> >  > >
> >  > > Date: Sat, 12 Feb 2011 03:33:15 +1100
> >  > > From: mark.abra...@anu.edu.au
> >  > > To: gmx-users@gromacs.org
> >  > > Subject: Re: [gmx-users] Add custom residue to DNA index group
> >  > >
> >  > >
> >  > >
> >  > >
> >  > >
> >  > >
> >  > >
> >  > > Message body
> >  > >
> >  > >
> >  > > On 12/02/2011 3:14 AM, william Stebbeds wrote:
> >  > >
> >  > >
> >  > > Hi Folks,
> >  > >
> >  > >
> >  > >
> >  > > I have added a custom DNA residue to the amber99sb ff, and
> >  > > everything works perfectly, (thanks to Justin!).
> >  > >
> >  > >
> >  > >
> >  > > The residue is incorporated perfectly into the sequence, with no
> >  > > abnormal events during simulations. I have updated all the files
> >  > > to include the new residue.
> >  > >
> >  > >
> >  > >
> >  > > I have since realised, when using g_rms, that my custom residue is
> >  > > not included in the default DNA index group, and appears as a
> >  > > group on its own.
> >  > >
> >  > >
> >  > >
> >  > > Is there a way of making gromacs understand that this residue is
> >  > > DNA when it makes the index files?
> >  > >
> >  > >
> >  > >
> >  > > I am not using make_ndx, I just let gromacs split the groups.
> >  > >
> >  > >
> >  > >
> >  > > Thanks in advance
> >  > >
> >  > >
> >  > >
> >  > > Will - Cranfield University
> >  > >
> >  > >
> >  > >
> >  > >
> >  > > You need to arrange for the tools to access a modified form of
> >  > > share/gromacs/top/residuetypes.dat with your custom residue suitably
> >  > > classified. I understand you can copy that file to your working
> >  > > directory and modify it there, and GROMACS will use the local copy.
> >  > >
> >  > >
> >  > >
> >  > > Mark
> >  > >
> >  > >
> >  > >
> >  > >
> >  > > --
> >  > > gmx-users mailing list gmx-users@gromacs.org
> >  > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >  > > Please search the archive at
> >  > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >  > > Please don't post (un)subscribe requests to the list. Use the
> >  > > www interface or send it to gmx-users-requ...@gromacs.org.
> >  > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >  > > --
> >  > > gmx-users mailing list gmx-users@gromacs.org
> >  > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >  > > Please search the archive at
> >  > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >  > > Please don't post (un)subscribe requests to the list. Use the
> >  > > www interface or send it to gmx-users-requ...@gromacs.org.
> >  > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >  >
> >  >
> >  >
> >  > --
> >  > gmx-users mailing list gmx-users@gromacs.org
> >  > ht

[gmx-users] Terminus Atoms genrestr?

[TJ Mustard]

  

  
Hi all,




Does anyone know how to make a positional restraint file for the terminal atoms in a protein/rna/dna chain via genrestr? I know I can get the backbone, C-alpha, etc.

 

Doing this by hand will be time consuming, and if there was an automated way of doing this I would be very happy.




 

Thank you,

TJ Mustard

  

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Add custom residue to DNA index group

[Justin A. Lemkul]

william Stebbeds wrote:

I made the changes to ../gromacs/top/residuetypes.dat

the Make_ndx output:

  0 System  : 34023 atoms
  1 DNA :   650 atoms
  2 DGO :66 atoms
  3 K   :43 atoms
  4 CL  :21 atoms
  5 Other   :66 atoms
  6 DGO :66 atoms
  7 K   :43 atoms
  8 CL  :21 atoms
  9 Ion :64 atoms
 10 DGO :66 atoms
 11 K   :43 atoms
 12 CL  :21 atoms
 13 Water   : 33243 atoms
 14 SOL : 33243 atoms
 15 non-Water   :   780 atoms
 16 Water_and_ions  : 33307 atoms

This system consists of a 22 residue DNA molecule, two of which are DGO, 
each have 33 atoms.


I also do not understand why DGO is repeated three times.



There have been significant changes to the generation of default groups for 
indexing since the 4.0.x series.  I would suggest you upload your input files 
and a description of the problem to the Redmine system so it can be investigated 
and fixed.  I've seen the same issue with duplicate moleculetypes, which looks 
like it's happening for several species here.  It's definitely something worth 
fixing.


http://redmine.gromacs.org/

For now, you can just merge DNA and DGO and create a complete index group.

-Justin


Thanks again

will


 > Date: Fri, 11 Feb 2011 12:08:52 -0500
 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] Add custom residue to DNA index group
 >
 >
 >
 > william Stebbeds wrote:
 > > Indeed I did
 > >
 > > DGO DNA
 > >
 >
 > Did you make the change system-wide, or in a local directory? If the 
latter,
 > you have to issue all your commands in that same directory or else 
the default

 > residuetypes.dat (in GMXLIB) will be read.
 >
 > Can you post the make_ndx output (i.e. list of groups)?
 >
 > -Justin
 >
 > > Cheers
 > >
 > > Will
 > >
 > > > Date: Fri, 11 Feb 2011 17:57:32 +0100
 > > > Subject: RE: [gmx-users] Add custom residue to DNA index group
 > > > From: dsar...@gwdg.de
 > > > To: gmx-users@gromacs.org
 > > >
 > > > >
 > > > > Thanks for the quick reply,
 > > > >
 > > > > I have already done that, and GROMACS, in all other cases, 
knows it is

 > > > > DNA, as it automatically forms the bonds with other residues.
 > > > >
 > > > > it is only when it makes its index files that it doesnt know 
that my

 > > > > residue is DNA.
 > > > >
 > > >
 > > > Did you make the change in residuetypes.dat file.
 > > > add your residues XXX as DNA in the residuetypes.dat file
 > > >
 > > > eq: XXX DNA
 > > >
 > > >
 > > >
 > > > Best Wishes,
 > > >
 > > > Sarath
 > > > > Cheers
 > > > >
 > > > > Will
 > > > >
 > > > >
 > > > >
 > > > >
 > > > >
 > > > >
 > > > > Date: Sat, 12 Feb 2011 03:33:15 +1100
 > > > > From: mark.abra...@anu.edu.au
 > > > > To: gmx-users@gromacs.org
 > > > > Subject: Re: [gmx-users] Add custom residue to DNA index group
 > > > >
 > > > >
 > > > >
 > > > >
 > > > >
 > > > >
 > > > >
 > > > > Message body
 > > > >
 > > > >
 > > > > On 12/02/2011 3:14 AM, william Stebbeds wrote:
 > > > >
 > > > >
 > > > > Hi Folks,
 > > > >
 > > > >
 > > > >
 > > > > I have added a custom DNA residue to the amber99sb ff, and
 > > > > everything works perfectly, (thanks to Justin!).
 > > > >
 > > > >
 > > > >
 > > > > The residue is incorporated perfectly into the sequence, with no
 > > > > abnormal events during simulations. I have updated all the files
 > > > > to include the new residue.
 > > > >
 > > > >
 > > > >
 > > > > I have since realised, when using g_rms, that my custom residue is
 > > > > not included in the default DNA index group, and appears as a
 > > > > group on its own.
 > > > >
 > > > >
 > > > >
 > > > > Is there a way of making gromacs understand that this residue is
 > > > > DNA when it makes the index files?
 > > > >
 > > > >
 > > > >
 > > > > I am not using make_ndx, I just let gromacs split the groups.
 > > > >
 > > > >
 > > > >
 > > > > Thanks in advance
 > > > >
 > > > >
 > > > >
 > > > > Will - Cranfield University
 > > > >
 > > > >
 > > > >
 > > > >
 > > > > You need to arrange for the tools to access a modified form of
 > > > > share/gromacs/top/residuetypes.dat with your custom residue 
suitably

 > > > > classified. I understand you can copy that file to your working
 > > > > directory and modify it there, and GROMACS will use the local copy.
 > > > >
 > > > >
 > > > >
 > > > > Mark
 > > > >
 > > > >
 > > > >
 > > > >
 > > > > --
 > > > > gmx-users mailing list gmx-users@gromacs.org
 > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > > > > Please search the archive at
 > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 > > > > Please don't post (un)subscribe requests to the list. Use the
 > > > > www interface or send it to gmx-users-requ...@gromacs.org.
 > > > > Can't post? Read http://www.gromacs.o

Re: [gmx-users] Terminus Atoms genrestr?

[Justin A. Lemkul]

TJ Mustard wrote:



Hi all,


Does anyone know how to make a positional restraint file for the 
terminal atoms in a protein/rna/dna chain via genrestr? I know I can get 
the backbone, C-alpha, etc.


 

Doing this by hand will be time consuming, and if there was an automated 
way of doing this I would be very happy.





Like the other Gromacs utilities, genrestr can make use of index files.

-Justin

 


Thank you,

TJ Mustard



--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

RE: [gmx-users] Add custom residue to DNA index group

[william Stebbeds]

Ok, will do.
Thanks very much
Will
> Date: Fri, 11 Feb 2011 13:29:53 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Add custom residue to DNA index group
> 
> 
> 
> william Stebbeds wrote:
> > I made the changes to ../gromacs/top/residuetypes.dat
> > 
> > the Make_ndx output:
> > 
> >   0 System  : 34023 atoms
> >   1 DNA :   650 atoms
> >   2 DGO :66 atoms
> >   3 K   :43 atoms
> >   4 CL  :21 atoms
> >   5 Other   :66 atoms
> >   6 DGO :66 atoms
> >   7 K   :43 atoms
> >   8 CL  :21 atoms
> >   9 Ion :64 atoms
> >  10 DGO :66 atoms
> >  11 K   :43 atoms
> >  12 CL  :21 atoms
> >  13 Water   : 33243 atoms
> >  14 SOL : 33243 atoms
> >  15 non-Water   :   780 atoms
> >  16 Water_and_ions  : 33307 atoms
> > 
> > This system consists of a 22 residue DNA molecule, two of which are DGO, 
> > each have 33 atoms.
> > 
> > I also do not understand why DGO is repeated three times.
> > 
> 
> There have been significant changes to the generation of default groups for 
> indexing since the 4.0.x series.  I would suggest you upload your input files 
> and a description of the problem to the Redmine system so it can be 
> investigated 
> and fixed.  I've seen the same issue with duplicate moleculetypes, which 
> looks 
> like it's happening for several species here.  It's definitely something 
> worth 
> fixing.
> 
> http://redmine.gromacs.org/
> 
> For now, you can just merge DNA and DGO and create a complete index group.
> 
> -Justin
> 
> > Thanks again
> > 
> > will
> > 
> > 
> >  > Date: Fri, 11 Feb 2011 12:08:52 -0500
> >  > From: jalem...@vt.edu
> >  > To: gmx-users@gromacs.org
> >  > Subject: Re: [gmx-users] Add custom residue to DNA index group
> >  >
> >  >
> >  >
> >  > william Stebbeds wrote:
> >  > > Indeed I did
> >  > >
> >  > > DGO DNA
> >  > >
> >  >
> >  > Did you make the change system-wide, or in a local directory? If the 
> > latter,
> >  > you have to issue all your commands in that same directory or else 
> > the default
> >  > residuetypes.dat (in GMXLIB) will be read.
> >  >
> >  > Can you post the make_ndx output (i.e. list of groups)?
> >  >
> >  > -Justin
> >  >
> >  > > Cheers
> >  > >
> >  > > Will
> >  > >
> >  > > > Date: Fri, 11 Feb 2011 17:57:32 +0100
> >  > > > Subject: RE: [gmx-users] Add custom residue to DNA index group
> >  > > > From: dsar...@gwdg.de
> >  > > > To: gmx-users@gromacs.org
> >  > > >
> >  > > > >
> >  > > > > Thanks for the quick reply,
> >  > > > >
> >  > > > > I have already done that, and GROMACS, in all other cases, 
> > knows it is
> >  > > > > DNA, as it automatically forms the bonds with other residues.
> >  > > > >
> >  > > > > it is only when it makes its index files that it doesnt know 
> > that my
> >  > > > > residue is DNA.
> >  > > > >
> >  > > >
> >  > > > Did you make the change in residuetypes.dat file.
> >  > > > add your residues XXX as DNA in the residuetypes.dat file
> >  > > >
> >  > > > eq: XXX DNA
> >  > > >
> >  > > >
> >  > > >
> >  > > > Best Wishes,
> >  > > >
> >  > > > Sarath
> >  > > > > Cheers
> >  > > > >
> >  > > > > Will
> >  > > > >
> >  > > > >
> >  > > > >
> >  > > > >
> >  > > > >
> >  > > > >
> >  > > > > Date: Sat, 12 Feb 2011 03:33:15 +1100
> >  > > > > From: mark.abra...@anu.edu.au
> >  > > > > To: gmx-users@gromacs.org
> >  > > > > Subject: Re: [gmx-users] Add custom residue to DNA index group
> >  > > > >
> >  > > > >
> >  > > > >
> >  > > > >
> >  > > > >
> >  > > > >
> >  > > > >
> >  > > > > Message body
> >  > > > >
> >  > > > >
> >  > > > > On 12/02/2011 3:14 AM, william Stebbeds wrote:
> >  > > > >
> >  > > > >
> >  > > > > Hi Folks,
> >  > > > >
> >  > > > >
> >  > > > >
> >  > > > > I have added a custom DNA residue to the amber99sb ff, and
> >  > > > > everything works perfectly, (thanks to Justin!).
> >  > > > >
> >  > > > >
> >  > > > >
> >  > > > > The residue is incorporated perfectly into the sequence, with no
> >  > > > > abnormal events during simulations. I have updated all the files
> >  > > > > to include the new residue.
> >  > > > >
> >  > > > >
> >  > > > >
> >  > > > > I have since realised, when using g_rms, that my custom residue is
> >  > > > > not included in the default DNA index group, and appears as a
> >  > > > > group on its own.
> >  > > > >
> >  > > > >
> >  > > > >
> >  > > > > Is there a way of making gromacs understand that this residue is
> >  > > > > DNA when it makes the index files?
> >  > > > >
> >  > > > >
> >  > > > >
> >  > > > > I am not using make_ndx, I just let gromacs split the groups.
> >  > > > >
> >  > > > >
> >  > > > >
> >  > > > > Thanks in advance
> >  > > > >
> >  > > > >
> >  > > > >
> >  > > > > Will - Cranfield University
> >  > > > >
> >  > > > 

Re: [gmx-users] Terminus Atoms genrestr?

[TJ Mustard]

  

  
Justin,




Yes but how can I automatically select the terminal residue's alpha carbons, without having to individually select residues?

 

Read the manual and some internet pages and found that you can easily select the alpha carbons on select residues by specifying them with the argument r_#_#_#_#_#_#... etc in make_ndx, which can then be used to make a positional restrain file via makerestr. I am just hoping there is a better, more automated way of doing this.

 

 

Thank you,

TJ Mustard



  On February 11, 2011 at 10:30 AM "Justin A. Lemkul"  wrote:
  
  >
  >
  > TJ Mustard wrote:
  > >
  > >
  > > Hi all,
  > >
  > >
  > > Does anyone know how to make a positional restraint file for the
  > > terminal atoms in a protein/rna/dna chain via genrestr? I know I can get
  > > the backbone, C-alpha, etc.
  > >
  > > 
  > >
  > > Doing this by hand will be time consuming, and if there was an automated
  > > way of doing this I would be very happy.
  > >
  > >
  >
  > Like the other Gromacs utilities, genrestr can make use of index files.
  >
  > -Justin
  >
  > > 
  > >
  > > Thank you,
  > >
  > > TJ Mustard
  > >
  >
  > --
  > 
  >
  > Justin A. Lemkul
  > Ph.D. Candidate
  > ICTAS Doctoral Scholar
  > MILES-IGERT Trainee
  > Department of Biochemistry
  > Virginia Tech
  > Blacksburg, VA
  > jalemkul[at]vt.edu | (540) 231-9080
  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
  >
  > 
  > --
  > gmx-users mailing list    gmx-users@gromacs.org
  > http://lists.gromacs.org/mailman/listinfo/gmx-users
  > Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
  > Please don't post (un)subscribe requests to the list. Use the
  > www interface or send it to gmx-users-requ...@gromacs.org.
  > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
  >


 

TJ Mustard
Email: musta...@onid.orst.edu
  

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Re: [gmx-users] Terminus Atoms genrestr?

[Justin A. Lemkul]

TJ Mustard wrote:



Justin,


Yes but how can I automatically select the terminal residue's alpha 
carbons, without having to individually select residues?


 

Read the manual and some internet pages and found that you can easily 
select the alpha carbons on select residues by specifying them with the 
argument r_#_#_#_#_#_#... etc in make_ndx, which can then be used to 
make a positional restrain file via makerestr. I am just hoping there is 
a better, more automated way of doing this.


 


I don't know of any Gromacs tool (other than pdb2gmx) that is smart enough to 
determine terminal residues on its own.  If you have multiple copies of the same 
molecule, then you know how many atoms are in each, so you can script a little 
loop that will do it for you, otherwise I don't think there's anything that will 
do this job on its own.  Maybe g_select, but its capabilities and syntax are not 
yet well-documented.


-Justin



 


Thank you,

TJ Mustard

On February 11, 2011 at 10:30 AM "Justin A. Lemkul"  wrote:

 >
 >
 > TJ Mustard wrote:
 > >
 > >
 > > Hi all,
 > >
 > >
 > > Does anyone know how to make a positional restraint file for the
 > > terminal atoms in a protein/rna/dna chain via genrestr? I know I 
can get

 > > the backbone, C-alpha, etc.
 > >
 > > 
 > >
 > > Doing this by hand will be time consuming, and if there was an 
automated

 > > way of doing this I would be very happy.
 > >
 > >
 >
 > Like the other Gromacs utilities, genrestr can make use of index files.
 >
 > -Justin
 >
 > > 
 > >

 > > Thank you,
 > >
 > > TJ Mustard
 > >
 >
 > --
 > 
 >
 > Justin A. Lemkul
 > Ph.D. Candidate
 > ICTAS Doctoral Scholar
 > MILES-IGERT Trainee
 > Department of Biochemistry
 > Virginia Tech
 > Blacksburg, VA
 > jalemkul[at]vt.edu | (540) 231-9080
 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >
 > 
 > --
 > gmx-users mailing listgmx-users@gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!

 > Please don't post (un)subscribe requests to the list. Use the
 > www interface or send it to gmx-users-requ...@gromacs.org.
 > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 >

 


TJ Mustard
Email: musta...@onid.orst.edu



--


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


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Re: [gmx-users] Terminus Atoms genrestr?

[TJ Mustard]

  

  
Justin,

 

Ok, if I find a way I will post it back here. And thank you for the recommendations.


 

Thank you,

TJ Mustard



  On February 11, 2011 at 11:05 AM "Justin A. Lemkul"  wrote:
  
  >
  >
  > TJ Mustard wrote:
  > >
  > >
  > > Justin,
  > >
  > >
  > > Yes but how can I automatically select the terminal residue's alpha
  > > carbons, without having to individually select residues?
  > >
  > > 
  > >
  > > Read the manual and some internet pages and found that you can easily
  > > select the alpha carbons on select residues by specifying them with the
  > > argument r_#_#_#_#_#_#... etc in make_ndx, which can then be used to
  > > make a positional restrain file via makerestr. I am just hoping there is
  > > a better, more automated way of doing this.
  > >
  > > 
  >
  > I don't know of any Gromacs tool (other than pdb2gmx) that is smart enough to
  > determine terminal residues on its own.  If you have multiple copies of the same
  > molecule, then you know how many atoms are in each, so you can script a little
  > loop that will do it for you, otherwise I don't think there's anything that will
  > do this job on its own.  Maybe g_select, but its capabilities and syntax are not
  > yet well-documented.
  >
  > -Justin
  >
  > >
  > > 
  > >
  > > Thank you,
  > >
  > > TJ Mustard
  > >
  > > On February 11, 2011 at 10:30 AM "Justin A. Lemkul"  wrote:
  > >
  > >  >
  > >  >
  > >  > TJ Mustard wrote:
  > >  > >
  > >  > >
  > >  > > Hi all,
  > >  > >
  > >  > >
  > >  > > Does anyone know how to make a positional restraint file for the
  > >  > > terminal atoms in a protein/rna/dna chain via genrestr? I know I
  > > can get
  > >  > > the backbone, C-alpha, etc.
  > >  > >
  > >  > >
  > >  > >
  > >  > > Doing this by hand will be time consuming, and if there was an
  > > automated
  > >  > > way of doing this I would be very happy.
  > >  > >
  > >  > >
  > >  >
  > >  > Like the other Gromacs utilities, genrestr can make use of index files.
  > >  >
  > >  > -Justin
  > >  >
  > >  > >
  > >  > >
  > >  > > Thank you,
  > >  > >
  > >  > > TJ Mustard
  > >  > >
  > >  >
  > >  > --
  > >  > 
  > >  >
  > >  > Justin A. Lemkul
  > >  > Ph.D. Candidate
  > >  > ICTAS Doctoral Scholar
  > >  > MILES-IGERT Trainee
  > >  > Department of Biochemistry
  > >  > Virginia Tech
  > >  > Blacksburg, VA
  > >  > jalemkul[at]vt.edu | (540) 231-9080
  > >  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
  > >  >
  > >  > 
  > >  > --
  > >  > gmx-users mailing list    gmx-users@gromacs.org
  > >  > http://lists.gromacs.org/mailman/listinfo/gmx-users
  > >  > Please search the archive at
  > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
  > >  > Please don't post (un)subscribe requests to the list. Use the
  > >  > www interface or send it to gmx-users-requ...@gromacs.org.
  > >  > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
  > >  >
  > >
  > > 
  > >
  > > TJ Mustard
  > > Email: musta...@onid.orst.edu
  > >
  >
  > --
  > 
  >
  > Justin A. Lemkul
  > Ph.D. Candidate
  > ICTAS Doctoral Scholar
  > MILES-IGERT Trainee
  > Department of Biochemistry
  > Virginia Tech
  > Blacksburg, VA
  > jalemkul[at]vt.edu | (540) 231-9080
  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
  >
  > 
  > --
  > gmx-users mailing list    gmx-users@gromacs.org
  > http://lists.gromacs.org/mailman/listinfo/gmx-users
  > Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
  > Please don't post (un)subscribe requests to the list. Use the
  > www interface or send it to gmx-users-requ...@gromacs.org.
  > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
  >


 

TJ Mustard
Email: musta...@onid.orst.edu
  

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Re: [gmx-users] Terminus Atoms genrestr?

[Teemu Murtola]

Hi,

On Fri, Feb 11, 2011 at 21:05, Justin A. Lemkul  wrote:
> I don't know of any Gromacs tool (other than pdb2gmx) that is smart enough
> to determine terminal residues on its own.  If you have multiple copies of
> the same molecule, then you know how many atoms are in each, so you can
> script a little loop that will do it for you, otherwise I don't think
> there's anything that will do this job on its own.  Maybe g_select, but its
> capabilities and syntax are not yet well-documented.

If your terminal residues have some atoms that are not present in any
other residues (e.g., OXT could be such an atom name), you can try to
achieve what you want with g_select with a selection like (for alpha
carbons of the terminal residues)
  name CA and same residue as name OXT

@Justin: If you have concrete suggestions on how the documentation
could be improved, I would be happy to hear them, and consider them
when I have time to think about the documentation.  I do agree that
it's not perfect, and this has been, in part, a conscious decision.
This is because g_select can really make use of only part of the
capabilities of the selection syntax, and currently there are no other
tool that uses selections at all.  Writing a complete documentation of
the selection syntax would require writing a lot of text that would
have very little use in the present version, and could just serve to
confuse people more.  Partial documentation that would only cover
g_select would probably need to be largely rewritten to cover
everything later, so this has not been very high on the priority list
either.  Still, the only critique I've heard so far (from several
people, it seems) is a vague "the documentation sucks", which doesn't
really help in improving things, or even figuring out where people
face problems.  g_select does provide some on-line help (by typing
"help" in the selection prompt), which should at least briefly
describe the syntax.

BR,
Teemu
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Re: [gmx-users] Terminus Atoms genrestr?

[Justin A. Lemkul]

Teemu Murtola wrote:

Hi,

On Fri, Feb 11, 2011 at 21:05, Justin A. Lemkul  wrote:

I don't know of any Gromacs tool (other than pdb2gmx) that is smart enough
to determine terminal residues on its own.  If you have multiple copies of
the same molecule, then you know how many atoms are in each, so you can
script a little loop that will do it for you, otherwise I don't think
there's anything that will do this job on its own.  Maybe g_select, but its
capabilities and syntax are not yet well-documented.


If your terminal residues have some atoms that are not present in any
other residues (e.g., OXT could be such an atom name), you can try to
achieve what you want with g_select with a selection like (for alpha
carbons of the terminal residues)
  name CA and same residue as name OXT

@Justin: If you have concrete suggestions on how the documentation
could be improved, I would be happy to hear them, and consider them
when I have time to think about the documentation.  I do agree that
it's not perfect, and this has been, in part, a conscious decision.
This is because g_select can really make use of only part of the
capabilities of the selection syntax, and currently there are no other
tool that uses selections at all.  Writing a complete documentation of
the selection syntax would require writing a lot of text that would
have very little use in the present version, and could just serve to
confuse people more.  Partial documentation that would only cover
g_select would probably need to be largely rewritten to cover
everything later, so this has not been very high on the priority list
either.  Still, the only critique I've heard so far (from several
people, it seems) is a vague "the documentation sucks", which doesn't
really help in improving things, or even figuring out where people
face problems.  g_select does provide some on-line help (by typing
"help" in the selection prompt), which should at least briefly
describe the syntax.



I didn't mean for that comment to be a criticism at all, and I'm sorry that it 
came off that way.  I know there are many users who (as we've seen on the list 
in the past) wish that g_select was magic and they treat it as such, so I simply 
meant it as a caution that some time investment would be necessary to make 
proper use of the program.  I certainly know you're busy doing very important 
things for Gromacs development and we all appreciate that.  Looking through the 
recent source I can tell that a lot of effort has gone into improving 
everything, in general.


One thing that I always hope to help with is documentation and learning 
material, and as such, I am trying to explore some of the new features and tools 
and hopefully I can help in maintaining this stuff, as well.


Hopefully I'll have some concrete suggestions in the future, and I certainly 
didn't mean to imply that anything sucks :)


-Justin


BR,
Teemu


--


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


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[gmx-users] genbox error

[Rini Gupta]

Dear gmx users,

I am using gromacs (version 4.0.7) 
to setup a 2-butoxyethanol-water simulation.
I created topology and coordinate file (.pdb) for BE using AUTOMATED TOPOLOGY 
BUILDER server.
It created a topology file (for united atom) compatible with GROMOS ffG53a6 
forcefield.
I want to generate a box containing 20 BE and 480 water molecules using
genbox but it fails to do so. It generates a box only with 1 BE instead of 20 
but successfully adding requested no. of water molecules. 

I used the following command:


genbox_d_mpi -cp conf.gro -cs spc216.gro -p topol.top -box 2.7 2.7 2.7  -ci 
conf.gro -nmol 19 -maxsol 480 -o out.gro

Then  I got the mesaage:

Reading solute configuration
UNITED ATOM STRUCTURE FOR MOLECULE
Containing 9 atoms in 1 residues
Initialising van der waals distances...
Reading molecule configuration 
UNITED ATOM STRUCTURE FOR MOLECULE
Containing 9 atoms in 1 residue
Initialising van der waals distances...
Try 5699
Added 0 molecules (out of 19 requested) of G2
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 2x2x2 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
SOL (   3 atoms):  1728 residues
Calculating Overlap...
box_margin = 0.315
Removed 1992 atoms that were outside the box
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's:   NS: 0.45   Coulomb: 0.45   LJ: 0.45
System total charge: 0.000
Grid: 8 x 8 x 8 cells
Succesfully made neighbourlist
nri = 10648, nrj = 270745
Checking Protein-Solvent overlap: tested 509 pairs, removed 72 atoms.
Checking Solvent-Solvent overlap: tested 39413 pairs, removed 738 atoms.
Added 480 molecules
Generated solvent containing 1440 atoms in 480 residues
Writing generated configuration to out.gro


While searching through mailing list I tried to do this in two separate steps 
i.e. but using -ci -nmol option and then solvating the box using -cs 
spc216.gro, but problem remain the same.
I also tried increasing -try option and increasing the box size but still it is 
creating box with only one solute BE instead od 20.

Can anyone please tell me what I am doing wrong here.

I using following topology file:

[ moleculetype ]
; Name   nrexcl
G269  3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  chargemasstotal_charge
1OE1G2OE 1   -0.345  15.9994
2   CH21G2C  10.151  14.0270
3   CH21G2C  10.194  14.0270  ;  0.000
4   CH21G2C  20.231  14.0270
5OA1G2O  2   -0.617  15.9994
6 H1G2H  20.386   1.0080  ;  0.000
7   CH21G2C  3   -0.035  14.0270
8   CH21G2C  30.143  14.0270
9   CH31G2CA 3   -0.108  15.0350  ; -0.000
; total charge of the molecule:   0.000
[ bonds ]
;  ai   aj  funct   c0 c1
122   0.1430   8.1800e+06
132   0.1430   8.1800e+06
242   0.1520   5.4300e+06
372   0.1520   5.4300e+06
452   0.1430   8.1800e+06
562   0.1000   2.3200e+07
782   0.1530   7.1500e+06
892   0.1530   7.1500e+06
[ pairs ]
;  ai   aj  funct  ;  all 1-4 pairs but the ones excluded in GROMOS itp
151
181
261
271
341
391
[ angles ]
;  ai   aj   ak  funct   angle fc
2132109.50   380.00
1242109.50   320.00
1372109.50   320.00
2452111.00   530.00
4562108.53   443.00
3782111.00   530.00
7892111.00   530.00
[ dihedrals ]
; GROMOS improper dihedrals
;  ai   aj   ak   al  funct   angle fc
[ dihedrals ]
;  ai   aj   ak   al  functph0  cp mult
31241  0.00 1.263
21371  0.00 1.263
12451  0.00 2.533
13781  0.00 3.773
24561  0.00 1.263
37891  0.00 3.773
[ exclusions ]
;  ai   aj  funct  ;  GROMOS 1-4 exclusions
 

Thanks and Regards,
Rini




Dr. Rini Gupta
Postdoctoral Fellow
University of British Columbia
Vancouver

 

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Re: [gmx-users] doubts on g_confrms output

[Mark Abraham]

On 12/02/2011 3:45 AM, Kwee Hong wrote:

Hi Mark,

I tried but with this error:

Fatal error:
Number of atoms in pdb frame 0 is 331 instead of 491


OK. I don't know why two frames with different numbers of atoms are 
written. Maybe g_confrms -one is useful. Or you can chop apart the PDB 
by hand in a text editor.


Mark



*From:* Mark Abraham 
*To:* Discussion list for GROMACS users 
*Sent:* Saturday, February 12, 2011 0:01:39
*Subject:* Re: [gmx-users] doubts on g_confrms output

On 12/02/2011 2:55 AM, Kwee Hong wrote:

Hi Tsjerk,

Thanks for the help. I got it.
But do you have any idea how to solve this in vmd?


Use trjconv -sep on the .pdb file to split it.

Mark



Regards,
Joyce


*From:* Tsjerk Wassenaar 
*To:* Discussion list for GROMACS users 
*Sent:* Saturday, January 22, 2011 15:53:22
*Subject:* Re: [gmx-users] doubts on g_confrms output

Hi Joyce,

In pymol use 'set all_states'

Cheers,

Tsjerk

On Jan 22, 2011 8:30 AM, "Kwee Hong" > wrote:


Hi,

I was trying to do some analysis following John's "GROMACS tutorial 
for solvation study of spider toxin peptide".

I'm using GROMACS-4.5.3 and my command line for g_confrms is

g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb

The program calculated the RMSD sucessfully and fit_wet.pdb was 
generated. Yet, when i tried to visualise fit_wet.pdb using VMD, the 
structure is obviously in a mess. And when I tried it out with 
pymol, I can only visualised one model. Model 2 did not appear. I 
wonder would it be the pdb format generated by g_confrms is not the 
standard pdb format and had caused VMD and final failed to read them?


Herein, I attached part of the pdb file generated by fit_wet.pdb. 
Any insight is welcomed.


Thanks,
Joyce



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Re: [gmx-users] genbox error

[Justin A. Lemkul]

Rini Gupta wrote:

Dear gmx users,

I am using gromacs (version 4.0.7)
to setup a 2-butoxyethanol-water simulation.
I created topology and coordinate file (.pdb) for BE using AUTOMATED 
TOPOLOGY BUILDER server.
It created a topology file (for united atom) compatible with GROMOS 
ffG53a6 forcefield.

I want to generate a box containing 20 BE and 480 water molecules using
genbox but it fails to do so. It generates a box only with 1 BE instead 
of 20 but successfully adding requested no. of water molecules.


I used the following command:


genbox_d_mpi -cp conf.gro -cs spc216.gro -p topol.top -box 2.7 2.7 2.7 
-ci conf.gro -nmol 19 -maxsol 480 -o out.gro




Do the -ci and -cs steps separately and see if that gives you the proper output. 
 I have found that the two are incompatible, but in theory, I don't know why 
one couldn't do everything in one step.


-Justin


Then I got the mesaage:

Reading solute configuration
UNITED ATOM STRUCTURE FOR MOLECULE
Containing 9 atoms in 1 residues
Initialising van der waals distances...
Reading molecule configuration
UNITED ATOM STRUCTURE FOR MOLECULE
Containing 9 atoms in 1 residue
Initialising van der waals distances...
Try 5699
Added 0 molecules (out of 19 requested) of G2
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 2x2x2 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 1728 residues
Calculating Overlap...
box_margin = 0.315
Removed 1992 atoms that were outside the box
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45
System total charge: 0.000
Grid: 8 x 8 x 8 cells
Succesfully made neighbourlist
nri = 10648, nrj = 270745
Checking Protein-Solvent overlap: tested 509 pairs, removed 72 atoms.
Checking Solvent-Solvent overlap: tested 39413 pairs, removed 738 atoms.
Added 480 molecules
Generated solvent containing 1440 atoms in 480 residues
Writing generated configuration to out.gro


While searching through mailing list I tried to do this in two separate 
steps i.e. but using -ci -nmol option and then solvating the box using 
-cs spc216.gro, but problem remain the same.
I also tried increasing -try option and increasing the box size but 
still it is creating box with only one solute BE instead od 20.


Can anyone please tell me what I am doing wrong here.

I using following topology file:

[ moleculetype ]
; Name nrexcl
G269 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass total_charge
1 OE 1 G2 OE 1 -0.345 15.9994
2 CH2 1 G2 C 1 0.151 14.0270
3 CH2 1 G2 C 1 0.194 14.0270 ; 0.000
4 CH2 1 G2 C 2 0.231 14.0270
5 OA 1 G2 O 2 -0.617 15.9994
6 H 1 G2 H 2 0.386 1.0080 ; 0.000
7 CH2 1 G2 C 3 -0.035 14.0270
8 CH2 1 G2 C 3 0.143 14.0270
9 CH3 1 G2 CA 3 -0.108 15.0350 ; -0.000
; total charge of the molecule: 0.000
[ bonds ]
; ai aj funct c0 c1
1 2 2 0.1430 8.1800e+06
1 3 2 0.1430 8.1800e+06
2 4 2 0.1520 5.4300e+06
3 7 2 0.1520 5.4300e+06
4 5 2 0.1430 8.1800e+06
5 6 2 0.1000 2.3200e+07
7 8 2 0.1530 7.1500e+06
8 9 2 0.1530 7.1500e+06
[ pairs ]
; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp
1 5 1
1 8 1
2 6 1
2 7 1
3 4 1
3 9 1
[ angles ]
; ai aj ak funct angle fc
2 1 3 2 109.50 380.00
1 2 4 2 109.50 320.00
1 3 7 2 109.50 320.00
2 4 5 2 111.00 530.00
4 5 6 2 108.53 443.00
3 7 8 2 111.00 530.00
7 8 9 2 111.00 530.00
[ dihedrals ]
; GROMOS improper dihedrals
; ai aj ak al funct angle fc
[ dihedrals ]
; ai aj ak al funct ph0 cp mult
3 1 2 4 1 0.00 1.26 3
2 1 3 7 1 0.00 1.26 3
1 2 4 5 1 0.00 2.53 3
1 3 7 8 1 0.00 3.77 3
2 4 5 6 1 0.00 1.26 3
3 7 8 9 1 0.00 3.77 3
[ exclusions ]
; ai aj funct ; GROMOS 1-4 exclusions


Thanks and Regards,
Rini




Dr. Rini Gupta
Postdoctoral Fellow
University of British Columbia
Vancouver








--


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


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Re: [gmx-users] Terminus Atoms genrestr?

[Mark Abraham]

On 12/02/2011 7:18 AM, Teemu Murtola wrote:

Still, the only critique I've heard so far (from several
people, it seems) is a vague "the documentation sucks", which doesn't
really help in improving things, or even figuring out where people
face problems.  g_select does provide some on-line help (by typing
"help" in the selection prompt), which should at least briefly
describe the syntax.


For some counter-evidence, there are some new MD users in my group 
who've asked me a million questions about stuff, but when told to use 
g_select to generate complex geometric selections about various buried 
and interstitial water molecules they've gone and done it without asking 
further.


Mark
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Re: [gmx-users] genbox error

[Mark Abraham]

On 12/02/2011 7:51 AM, Rini Gupta wrote:

Dear gmx users,

I am using gromacs (version 4.0.7)
to setup a 2-butoxyethanol-water simulation.
I created topology and coordinate file (.pdb) for BE using AUTOMATED 
TOPOLOGY BUILDER server.
It created a topology file (for united atom) compatible with GROMOS 
ffG53a6 forcefield.

I want to generate a box containing 20 BE and 480 water molecules using
genbox but it fails to do so. It generates a box only with 1 BE 
instead of 20 but successfully adding requested no. of water molecules.


I used the following command:


genbox_d_mpi -cp conf.gro -cs spc216.gro -p topol.top -box 2.7 2.7 2.7 
-ci conf.gro -nmol 19 -maxsol 480 -o out.gro


Then I got the mesaage:

Reading solute configuration
UNITED ATOM STRUCTURE FOR MOLECULE
Containing 9 atoms in 1 residues
Initialising van der waals distances...
Reading molecule configuration
UNITED ATOM STRUCTURE FOR MOLECULE
Containing 9 atoms in 1 residue
Initialising van der waals distances...
Try 5699
Added 0 molecules (out of 19 requested) of G2
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 2x2x2 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 1728 residues
Calculating Overlap...
box_margin = 0.315
Removed 1992 atoms that were outside the box
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45
System total charge: 0.000
Grid: 8 x 8 x 8 cells
Succesfully made neighbourlist
nri = 10648, nrj = 270745
Checking Protein-Solvent overlap: tested 509 pairs, removed 72 atoms.
Checking Solvent-Solvent overlap: tested 39413 pairs, removed 738 atoms.
Added 480 molecules
Generated solvent containing 1440 atoms in 480 residues
Writing generated configuration to out.gro


While searching through mailing list I tried to do this in two 
separate steps i.e. but using -ci -nmol option and then solvating the 
box using -cs spc216.gro, but problem remain the same.
I also tried increasing -try option and increasing the box size but 
still it is creating box with only one solute BE instead od 20.


You're definitely trying to do too many things in one operation. I suggest

1. Use editconf to define a suitably big box around a single BE molecule.

2. Use genbox -ci -nmol 19

3. Use genbox -cs -cp

Or use genconf -shuffle to replace 1 and 2 (but this is less random)

Mark



Can anyone please tell me what I am doing wrong here.

I using following topology file:

[ moleculetype ]
; Name nrexcl
G269 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass total_charge
1 OE 1 G2 OE 1 -0.345 15.9994
2 CH2 1 G2 C 1 0.151 14.0270
3 CH2 1 G2 C 1 0.194 14.0270 ; 0.000
4 CH2 1 G2 C 2 0.231 14.0270
5 OA 1 G2 O 2 -0.617 15.9994
6 H 1 G2 H 2 0.386 1.0080 ; 0.000
7 CH2 1 G2 C 3 -0.035 14.0270
8 CH2 1 G2 C 3 0.143 14.0270
9 CH3 1 G2 CA 3 -0.108 15.0350 ; -0.000
; total charge of the molecule: 0.000
[ bonds ]
; ai aj funct c0 c1
1 2 2 0.1430 8.1800e+06
1 3 2 0.1430 8.1800e+06
2 4 2 0.1520 5.4300e+06
3 7 2 0.1520 5.4300e+06
4 5 2 0.1430 8.1800e+06
5 6 2 0.1000 2.3200e+07
7 8 2 0.1530 7.1500e+06
8 9 2 0.1530 7.1500e+06
[ pairs ]
; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp
1 5 1
1 8 1
2 6 1
2 7 1
3 4 1
3 9 1
[ angles ]
; ai aj ak funct angle fc
2 1 3 2 109.50 380.00
1 2 4 2 109.50 320.00
1 3 7 2 109.50 320.00
2 4 5 2 111.00 530.00
4 5 6 2 108.53 443.00
3 7 8 2 111.00 530.00
7 8 9 2 111.00 530.00
[ dihedrals ]
; GROMOS improper dihedrals
; ai aj ak al funct angle fc
[ dihedrals ]
; ai aj ak al funct ph0 cp mult
3 1 2 4 1 0.00 1.26 3
2 1 3 7 1 0.00 1.26 3
1 2 4 5 1 0.00 2.53 3
1 3 7 8 1 0.00 3.77 3
2 4 5 6 1 0.00 1.26 3
3 7 8 9 1 0.00 3.77 3
[ exclusions ]
; ai aj funct ; GROMOS 1-4 exclusions


Thanks and Regards,
Rini




Dr. Rini Gupta
Postdoctoral Fellow
University of British Columbia
Vancouver




 





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Re: [gmx-users] Dangling phospholipids

[Dr. Ramón Garduño-Juárez]

Justin,

Regarding my question I forgot to tell you that after expanding the 
system 4X, we have performed 26 shrinking steps at the 0.95 rate.


The system we are working with is one in which we have embedded two 
proteins into the bilayer, one of them is a toxin and the other a 
putative channel. Both proteins are docked in some way.


The last lines of the last shrinking step are:
---
Area per protein: 10 nm^2
Area per lipid: 0.596104455536294 nm^2

Area per protein, upper half: 9 nm^2
Area per lipid, upper leaflet : 0.612233487794359 nm^2

Area per protein, lower half: 8.5 nm^2
Area per lipid, lower leaflet : 0.620298003923391 nm^2

Writing Area per lipid...
Done!
-

The area per lipid of DMPC has been reported to be between 0.40 to 0.703 
nm^2, with an average value of 0.656 nm^2


After visualizing of the system we found a that those lipid molecules at 
the four corners of the box as disordered. That is, one of their tails, 
or both, are far from the core of the bilayer. Nothing like the original 
lipid box.


Do you think that we have shinked too much, or as you said, we have not 
minimized long enough?


Cheers,
Ramon Garduno



El 09/02/2011 11:25 a.m., Justin A. Lemkul escribió:



Dr. Ramón Garduño-Juárez wrote:

Dear All,

First of all I want to tank Justin Lemkul and Thomas Piggot for their 
useful comments that helped me to resolve my previous questions 
regarding the construction of a lipid membrane.


Now I would like to post this question to this forum.

I got through placing a putative ion channel into a DPPC bilayer. I 
managed to expand this sytem -> minimize it -> shrink it (several 
times) -> minimize it (several times) until I got an adequate lipid 
density.


After viewing the final results I noticed that there are several 
lipid molecules that are dangling at the end of the periodic box.


Is this normal, or I did something wrong?. If this is expected, How 
do I get rid of the dangling lipid molecules before I start a MD 
simulation?




By "dangling" do you mean that they are somewhat isolated from the 
rest of the lipids?  If so, how many are there?  Usually this just 
indicates that you're not done shrinking the membrane back to 
appropriate dimensions.  The final box vectors achieved through 
shrinking should usually be fairly close to the original dimensions of 
the system.  If this is not the case, then you're not done building 
your system.


-Justin


Waiting for your replies...

Sincerely,
Ramon Garduno



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Re: [gmx-users] genbox error

[Mark Abraham]

On 12/02/2011 12:22 PM, Justin A. Lemkul wrote:
Do the -ci and -cs steps separately and see if that gives you the 
proper output.  I have found that the two are incompatible, but in 
theory, I don't know why one couldn't do everything in one step. 


It can depend on the assumptions about the purpose of -cs and -ci. If 
-ci is being used to insert some ions or small molecules then you want 
to do -cs first lest you create larger interstices via the VDW 
exclusions. If -ci inserts large molecules, then you want to do that 
first. The observations of the OP suggest the former is implemented.


Mark
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Re: [gmx-users] Dangling phospholipids

[Justin A. Lemkul]

Dr. Ramón Garduño-Juárez wrote:

Justin,

Regarding my question I forgot to tell you that after expanding the 
system 4X, we have performed 26 shrinking steps at the 0.95 rate.


The system we are working with is one in which we have embedded two 
proteins into the bilayer, one of them is a toxin and the other a 
putative channel. Both proteins are docked in some way.


The last lines of the last shrinking step are:
---
Area per protein: 10 nm^2
Area per lipid: 0.596104455536294 nm^2

Area per protein, upper half: 9 nm^2
Area per lipid, upper leaflet : 0.612233487794359 nm^2

Area per protein, lower half: 8.5 nm^2
Area per lipid, lower leaflet : 0.620298003923391 nm^2

Writing Area per lipid...
Done!
-

The area per lipid of DMPC has been reported to be between 0.40 to 0.703 
nm^2, with an average value of 0.656 nm^2


After visualizing of the system we found a that those lipid molecules at 
the four corners of the box as disordered. That is, one of their tails, 
or both, are far from the core of the bilayer. Nothing like the original 
lipid box.


Do you think that we have shinked too much, or as you said, we have not 
minimized long enough?




That's possible.  InflateGRO tends to overestimate the true area per lipid, so 
your DMPC may be compressed a bit more than you think.  I usually stop DPPC 
compression in the ballpark of 0.70 nm^2.  If the lipids are reasonably close to 
the rest of the system and not completely isolated in their own vacuum state, 
then a gentle equilibration can bring everything together within a few ns.


-Justin


Cheers,
Ramon Garduno



El 09/02/2011 11:25 a.m., Justin A. Lemkul escribió:



Dr. Ramón Garduño-Juárez wrote:

Dear All,

First of all I want to tank Justin Lemkul and Thomas Piggot for their 
useful comments that helped me to resolve my previous questions 
regarding the construction of a lipid membrane.


Now I would like to post this question to this forum.

I got through placing a putative ion channel into a DPPC bilayer. I 
managed to expand this sytem -> minimize it -> shrink it (several 
times) -> minimize it (several times) until I got an adequate lipid 
density.


After viewing the final results I noticed that there are several 
lipid molecules that are dangling at the end of the periodic box.


Is this normal, or I did something wrong?. If this is expected, How 
do I get rid of the dangling lipid molecules before I start a MD 
simulation?




By "dangling" do you mean that they are somewhat isolated from the 
rest of the lipids?  If so, how many are there?  Usually this just 
indicates that you're not done shrinking the membrane back to 
appropriate dimensions.  The final box vectors achieved through 
shrinking should usually be fairly close to the original dimensions of 
the system.  If this is not the case, then you're not done building 
your system.


-Justin


Waiting for your replies...

Sincerely,
Ramon Garduno





--


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


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Re:[gmx-users] genbox error

[Rini Gupta]

 Hello Mark,

Thanks for the reply.

I tried to first make a box using editconf
editconf_d_mpi -f conf.gro -o be.gro -bt cubic -box 2.7 2.7 2.7

Box is successfully created and then I use 

genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 19 -o out.gro

still, I  am getting only one BE molecule instead of 19.

 What can I do now? Is there possibilty that my .gro file is not correct.

Best Regards,
Rini
 
On Sat, 12 Feb 2011 06:58:49 +0530  wrote
>
  

  
  
On 12/02/2011 7:51 AM, Rini Gupta wrote:
Dear gmx users,

  

  I am using gromacs (version 4.0.7) 

  to setup a 2-butoxyethanol-water simulation.

  I created topology and coordinate file (.pdb) for BE using
  AUTOMATED TOPOLOGY BUILDER server.

  It created a topology file (for united atom) compatible with
  GROMOS ffG53a6 forcefield.

  I want to generate a box containing 20 BE and 480 water molecules
  using

  genbox but it fails to do so. It generates a box only with 1 BE
  instead of 20 but successfully adding requested no. of water
  molecules. 

  

  I used the following command:

  

  

  genbox_d_mpi -cp conf.gro -cs spc216.gro -p topol.top -box 2.7 2.7
  2.7 -ci conf.gro -nmol 19 -maxsol 480 -o out.gro

  

  Then I got the mesaage:

  

  Reading solute configuration

  UNITED ATOM STRUCTURE FOR MOLECULE

  Containing 9 atoms in 1 residues

  Initialising van der waals distances...

  Reading molecule configuration 

  UNITED ATOM STRUCTURE FOR MOLECULE

  Containing 9 atoms in 1 residue

  Initialising van der waals distances...

  Try 5699

  Added 0 molecules (out of 19 requested) of G2

  Reading solvent configuration

  "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR.
  1984"

  solvent configuration contains 648 atoms in 216 residues

  

  Initialising van der waals distances...

  Will generate new solvent configuration of 2x2x2 boxes

  Generating configuration

  Sorting configuration

  Found 1 molecule type:

  SOL ( 3 atoms): 1728 residues

  Calculating Overlap...

  box_margin = 0.315

  Removed 1992 atoms that were outside the box

  Neighborsearching with a cut-off of 0.45

  Table routines are used for coulomb: FALSE

  Table routines are used for vdw: FALSE

  Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45

  System total charge: 0.000

  Grid: 8 x 8 x 8 cells

  Succesfully made neighbourlist

  nri = 10648, nrj = 270745

  Checking Protein-Solvent overlap: tested 509 pairs, removed 72
  atoms.

  Checking Solvent-Solvent overlap: tested 39413 pairs, removed 738
  atoms.

  Added 480 molecules

  Generated solvent containing 1440 atoms in 480 residues

  Writing generated configuration to out.gro

  

  

  While searching through mailing list I tried to do this in two
  separate steps i.e. but using -ci -nmol option and then solvating
  the box using -cs spc216.gro, but problem remain the same.

  I also tried increasing -try option and increasing the box size
  but still it is creating box with only one solute BE instead od
  20.




You're definitely trying to do too many things in one operation. I
suggest



1. Use editconf to define a suitably big box around a single BE
molecule.



2. Use genbox -ci -nmol 19



3. Use genbox -cs -cp



Or use genconf -shuffle to replace 1 and 2 (but this is less random)



Mark




  

  Can anyone please tell me what I am doing wrong here.

  

  I using following topology file:

  

  [ moleculetype ]

  ; Name nrexcl

  G269 3

  [ atoms ]

  ; nr type resnr resid atom cgnr charge mass total_charge

  1 OE 1 G2 OE 1 -0.345 15.9994

  2 CH2 1 G2 C 1 0.151 14.0270

  3 CH2 1 G2 C 1 0.194 14.0270 ; 0.000

  4 CH2 1 G2 C 2 0.231 14.0270

  5 OA 1 G2 O 2 -0.617 15.9994

  6 H 1 G2 H 2 0.386 1.0080 ; 0.000

  7 CH2 1 G2 C 3 -0.035 14.0270

  8 CH2 1 G2 C 3 0.143 14.0270

  9 CH3 1 G2 CA 3 -0.108 15.0350 ; -0.000

  ; total charge of the molecule: 0.000

  [ bonds ]

  ; ai aj funct c0 c1

  1 2 2 0.1430 8.1800e+06

  1 3 2 0.1430 8.1800e+06

  2 4 2 0.1520 5.4300e+06

  3 7 2 0.1520 5.4300e+06

  4 5 2 0.1430 8.1800e+06

  5 6 2 0.1000 2.3200e+07

  7 8 2 0.1530 7.1500e+06

  8 9 2 0.1530 7.1500e+06

  [ pairs ]

  ; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp

  1 5 1

  1 8 1

  2 6 1

  2 7 1

  3 4 1

  3 9 1

  [ angles ]

  ; ai aj ak funct angle fc

  2 1 3 2 109.50 380.00

  1 2 4 2 109.50 320.00

  1 3 7 2 109.50 320.00

  2 4 5 2 111.00 530.00

  4 5 6 2 108.53 443.00

  3 7 8 2 111.00 530.00

  7

Re: [gmx-users] genbox error

[Mark Abraham]

On 12/02/2011 12:51 PM, Rini Gupta wrote:


Hello Mark,

Thanks for the reply.

I tried to first make a box using editconf
editconf_d_mpi -f conf.gro -o be.gro -bt cubic -box 2.7 2.7 2.7

Box is successfully created and then I use

genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 19 -o out.gro

still, I am getting only one BE molecule instead of 19.


Hmm that's strange. What was the terminal output?

Mark


What can I do now? Is there possibilty that my .gro file is not correct.

Best Regards,
Rini

On Sat, 12 Feb 2011 06:58:49 +0530 wrote
>




On 12/02/2011 7:51 AM, Rini Gupta wrote:
Dear gmx users,



I am using gromacs (version 4.0.7)

to setup a 2-butoxyethanol-water simulation.

I created topology and coordinate file (.pdb) for BE using
AUTOMATED TOPOLOGY BUILDER server.

It created a topology file (for united atom) compatible with
GROMOS ffG53a6 forcefield.

I want to generate a box containing 20 BE and 480 water molecules
using

genbox but it fails to do so. It generates a box only with 1 BE
instead of 20 but successfully adding requested no. of water
molecules.



I used the following command:





genbox_d_mpi -cp conf.gro -cs spc216.gro -p topol.top -box 2.7 2.7
2.7 -ci conf.gro -nmol 19 -maxsol 480 -o out.gro



Then I got the mesaage:



Reading solute configuration

UNITED ATOM STRUCTURE FOR MOLECULE

Containing 9 atoms in 1 residues

Initialising van der waals distances...

Reading molecule configuration

UNITED ATOM STRUCTURE FOR MOLECULE

Containing 9 atoms in 1 residue

Initialising van der waals distances...

Try 5699

Added 0 molecules (out of 19 requested) of G2

Reading solvent configuration

"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR.
1984"

solvent configuration contains 648 atoms in 216 residues



Initialising van der waals distances...

Will generate new solvent configuration of 2x2x2 boxes

Generating configuration

Sorting configuration

Found 1 molecule type:

SOL ( 3 atoms): 1728 residues

Calculating Overlap...

box_margin = 0.315

Removed 1992 atoms that were outside the box

Neighborsearching with a cut-off of 0.45

Table routines are used for coulomb: FALSE

Table routines are used for vdw: FALSE

Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45

System total charge: 0.000

Grid: 8 x 8 x 8 cells

Succesfully made neighbourlist

nri = 10648, nrj = 270745

Checking Protein-Solvent overlap: tested 509 pairs, removed 72
atoms.

Checking Solvent-Solvent overlap: tested 39413 pairs, removed 738
atoms.

Added 480 molecules

Generated solvent containing 1440 atoms in 480 residues

Writing generated configuration to out.gro





While searching through mailing list I tried to do this in two
separate steps i.e. but using -ci -nmol option and then solvating
the box using -cs spc216.gro, but problem remain the same.

I also tried increasing -try option and increasing the box size
but still it is creating box with only one solute BE instead od
20.




You're definitely trying to do too many things in one operation. I
suggest



1. Use editconf to define a suitably big box around a single BE
molecule.



2. Use genbox -ci -nmol 19



3. Use genbox -cs -cp



Or use genconf -shuffle to replace 1 and 2 (but this is less random)



Mark






Can anyone please tell me what I am doing wrong here.



I using following topology file:



[ moleculetype ]

; Name nrexcl

G269 3

[ atoms ]

; nr type resnr resid atom cgnr charge mass total_charge

1 OE 1 G2 OE 1 -0.345 15.9994

2 CH2 1 G2 C 1 0.151 14.0270

3 CH2 1 G2 C 1 0.194 14.0270 ; 0.000

4 CH2 1 G2 C 2 0.231 14.0270

5 OA 1 G2 O 2 -0.617 15.9994

6 H 1 G2 H 2 0.386 1.0080 ; 0.000

7 CH2 1 G2 C 3 -0.035 14.0270

8 CH2 1 G2 C 3 0.143 14.0270

9 CH3 1 G2 CA 3 -0.108 15.0350 ; -0.000

; total charge of the molecule: 0.000

[ bonds ]

; ai aj funct c0 c1

1 2 2 0.1430 8.1800e+06

1 3 2 0.1430 8.1800e+06

2 4 2 0.1520 5.4300e+06

3 7 2 0.1520 5.4300e+06

4 5 2 0.1430 8.1800e+06

5 6 2 0.1000 2.3200e+07

7 8 2 0.1530 7.1500e+06

8 9 2 0.1530 7.1500e+06

[ pairs ]

; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp

1 5 1

1 8 1

2 6 1

2 7 1

3 4 1

3 9 1

[ angles ]

; ai aj ak funct angle fc

2 1 3 2 109.50 380.00

1 2 4 2 109.50 320.00

1 3 7 2 109.50 320.00

2 4 5 2 111.00 530.00

4 5 6 2 108.53 443.00

3 7 8 2 111.00 530.00

7 8 9 2 111.00 530.00

[ dihedrals ]

; GROMOS improper dihedrals

; ai aj ak al funct angle fc

[ dihedrals ]

; ai aj ak al funct ph0 cp mult

3 1 2 4 1 0.00 1.26 3

2 1 3 7 1 0.00 1.26 3

1 2 4 5 1 0.00 2.53 3

1 3 7 8 1 0.00 3.77 3

2 4 5 6 1 0.00 1.26 3

3 7 8 9 1 0.00 3.77 3

[ exclusions ]

; ai aj funct ; GROMOS 1-4 exclusions





Thanks and Regards,

Rini









Dr. Rini Gupta

Postdoctoral Fellow

University of British Columbia

Vancouver





















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Re: Re: [gmx-users] genbox error

[Rini Gupta]

Hi,  

I am getting following output after using editconf to create  a box 
followed by
genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 2 -o out.gro

This time i tried to insert just 2 molecules still the command is not 
working.

---

Opening library file 
/global/software/gromacs/4.0.7/intel/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
 this can deviate from the real mass of the atom type
Opening library file 
/global/software/gromacs/4.0.7/intel/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
 this can deviate from the real mass of the atom type
Opening library file 
/global/software/gromacs/4.0.7/intel/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file 
/global/software/gromacs/4.0.7/intel/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file 
/global/software/gromacs/4.0.7/intel/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file 
/global/software/gromacs/4.0.7/intel/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading solute configuration
UNITED ATOM STRUCTURE FOR MOLECULE
Containing 9 atoms in 1 residues
Initialising van der waals distances...
Reading molecule configuration 
UNITED ATOM STRUCTURE FOR MOLECULE
Containing 9 atoms in 1 residue
Initialising van der waals distances...
Try 19
Added 0 molecules (out of 2 requested) of G2
Writing generated configuration to out.gro

Back Off! I just backed up out.gro to ./#out.gro.1#
UNITED ATOM STRUCTURE FOR MOLECULE

Output configuration contains 9 atoms in 1 residues
Volume :  19.683 (nm^3)
Density: 8.94928 (g/l)
Number of SOL molecules:  0   

Processing topology
--

Best Regards,
Rini




On Sat, 12 Feb 2011 08:07:27 +0530  wrote
>
  

  
  
On 12/02/2011 12:51 PM, Rini Gupta wrote:


  Hello Mark,

  

  Thanks for the reply.

  

  I tried to first make a box using editconf

  editconf_d_mpi -f conf.gro -o be.gro -bt cubic -box 2.7 2.7 2.7

  

  Box is successfully created and then I use 

  

  genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 19 -o
  out.gro

  

  still, I am getting only one BE molecule instead of 19.




Hmm that's strange. What was the terminal output?



Mark



 What can I do now? Is there possibilty that my .gro
  file is not correct.

  

  Best Regards,

  Rini

  

  On Sat, 12 Feb 2011 06:58:49 +0530 wrote

  >

  

  

  

  

  On 12/02/2011 7:51 AM, Rini Gupta wrote:

  Dear gmx users,

  

  

  

  I am using gromacs (version 4.0.7) 

  

  to setup a 2-butoxyethanol-water simulation.

  

  I created topology and coordinate file (.pdb) for BE using

  AUTOMATED TOPOLOGY BUILDER server.

  

  It created a topology file (for united atom) compatible with

  GROMOS ffG53a6 forcefield.

  

  I want to generate a box containing 20 BE and 480 water molecules

  using

  

  genbox but it fails to do so. It generates a box only with 1 BE

  instead of 20 but successfully adding requested no. of water

  molecules. 

  

  

  

  I used the following command:

  

  

  

  

  

  genbox_d_mpi -cp conf.gro -cs spc216.gro -p topol.top -box 2.7 
2.7

  2.7 -ci conf.gro -nmol 19 -maxsol 480 -o out.gro

  

  

  

  Then I got the mesaage:

  

  

  

  Reading solute configuration

  

  UNITED ATOM STRUCTURE FOR MOLECULE

  

  Containing 9 atoms in 1 residues

  

  Initialising van der waals distances...

  

  Reading molecule configuration 

  

  UNITED ATOM STRUCTURE FOR MOLECULE

  

  Containing 9 atoms in 1 residue

  

  Initialising van der waals distances...

  

  Try 5699

  

  Added 0 molecules (out of 19 requested) of G2

  

  Reading solvent configuration

  

  "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR.

  1984"

  

  solvent configuration contains 648 atoms in 216 residues

  

  

  

  Initialising van der waals distances...

  

  Will generate new solvent configuration of 2x2x2 boxes

  

  Generating configuration

  

  Sorting configuration

  

  Found 1 molecule type:

  

  SOL ( 3 atoms): 1728 residues

  

  Calculating Overlap...

  

  box_margin = 0.315

  

  Removed 1992 atoms that were outside the box

  

  Neighborsearching with a cut-off of 0.45

  

  Table routines are used for coulomb: FALSE

  

  Ta