Re: [gmx-users] Problem in implementing do_dssp

[Jianguo Li]

Maybe you could first try chmod +x dssp-2.0.4-linux-i386 , and then do_dssp.
 

On Thursday, 7 April 2016, 13:45, Rishikesh Parulekar 
 wrote:
 

 Hi justin Lemkul
dssp binary from usr/local/bin is working fine on its own but the command
it is showing for secondary structure determination is different i.e
dssp.exe  -i 1crn.pdb -o 1crn.dssp that means I am able to get output in
.dssp format not in .xpm format which is obtained from command : do_dssp -f
md.trr -s md.tpr -o ss.xpm. Howere with do_dssp module it shows flags
corresponding to -f and -s options.
dssp standalone binary is showing the version DSSP 2.0.4.

On Wed, Apr 6, 2016 at 10:56 PM, Rishikesh Parulekar <
rishi05parule...@gmail.com> wrote:

> dssp binaries are those which are obtained from site
> ftp://ftp.cmbi.ru.nl/pub/software/dssp ?
>
> On Wed, Apr 6, 2016 at 10:41 PM, Erik Marklund <
> erik.markl...@chem.ox.ac.uk> wrote:
>
>> Dear Rishikesh,
>>
>> No, you misunderstand. We don’t suggest to issue “do_dssp”, but to run
>> dssp, which you say is located in /usr/local/bin, to make sure it works the
>> way it should.
>>
>> Kind regards,
>> Erik
>>
>> > On 6 Apr 2016, at 18:08, Rishikesh Parulekar <
>> rishi05parule...@gmail.com> wrote:
>> >
>> > while running directly it shows do_dssp command not found.
>> >
>> >
>> > On Wed, Apr 6, 2016 at 10:29 PM, Justin Lemkul  wrote:
>> >
>> >>
>> >>
>> >> On 4/6/16 12:57 PM, Rishikesh Parulekar wrote:
>> >>
>> >>> Hi ErikMarklund,
>> >>>        Ya I have tested dssp as it shows all flags options with
>> gmx_mpi
>> >>> do_dssp -h that means executable is locatable but it is not giving
>> output
>> >>> after selecting group protein ends with fatal error : failed to
>> execute
>> >>> command. Try specifying your dssp version with the -ver option
>> >>>
>> >>>
>> >> Executing gmx do_dssp is not a valid test of whether or not your dssp
>> >> works. That just means your gmx binary is capable of displaying help
>> >> information. Please do as Erik and I both suggested and try to run the
>> dssp
>> >> binary directly, not via gmx do_dssp.
>> >>
>> >> -Justin
>> >>
>> >>
>> >> On Wed, Apr 6, 2016 at 10:14 PM, Rishikesh Parulekar <
>> >>> rishi05parule...@gmail.com> wrote:
>> >>>
>> >>> Hi Justin Lemkul,
>>  It works with gmx binary complied with mpi as u can see this is my
>>  command
>>  : gmx_mpi do_dssp -f md.trr -s md.tpr -o ss.xpm -sc protein.xvg -ver
>> 2 .
>>  After executing command I am able to select group for dssp
>> calculation
>>  but
>>  it ends with fatal error : failed to execute command. Try specifying
>> your
>>  dssp version with the -ver option
>> 
>>  On Wed, Apr 6, 2016 at 9:52 PM, Erik Marklund <
>>  erik.markl...@chem.ox.ac.uk
>> 
>> > wrote:
>> >
>> 
>>  Dear Rishikesh,
>> >
>> > And you have tested that your dssp runs properly on your computer?
>> Do
>> > you
>> > run do_dssp from a script? If so, can you please show the script and
>> > maybe
>> > someone spots something?
>> >
>> > Kind regards,
>> > Erik
>> >
>> > On 6 Apr 2016, at 17:03, Rishikesh Parulekar <
>> >>
>> > rishi05parule...@gmail.com> wrote:
>> >
>> >>
>> >> Hi all,
>> >> Is there any possible solution for my mentioned problem of do_dssp
>> >> implementation fatal error.
>> >>
>> >> regards
>> >>
>> >> On Wed, Apr 6, 2016 at 6:36 PM, Rishikesh Parulekar <
>> >> rishi05parule...@gmail.com> wrote:
>> >>
>> >> my error is not regarding the mismatch of name for the software.
>> It has
>> >>> recognised the software at usr/local/bin but it is showing fatal
>> error
>> >>>
>> >> : failed
>> >
>> >> to execute command. Try specifying your dssp version with the -ver
>> >>>
>> >> option.
>> >
>> >> If the problem is with path of software the error of setenv have
>> >>>
>> >> occured.
>> >
>> >> Hence I have mentioned the ver in the command : gmx_mpi do_dssp -f
>> >>>
>> >> md.trr
>> >
>> >> -s md.tpr -o ss.xpm -sc protein.xvg -ver 2 but still the same
>> error.
>> >>>
>> >>> On Wed, Apr 6, 2016 at 6:32 PM, Rishikesh Parulekar <
>> >>> rishi05parule...@gmail.com> wrote:
>> >>>
>> >>> dssp executable is directly downloaded from the
>>  ftp://ftp.cmbi.ru.nl/pub/software/dssp site and it has ready to
>> use
>>  executable file for version 2.0.4. So this is the case and it has
>> 
>> >>> been kept
>> >
>> >> under path /usr/local/bin with dssp name.
>> 
>>  On Wed, Apr 6, 2016 at 6:17 PM, Sarath Chandra <
>>  sarathchandrada...@gmail.com> wrote:
>> 
>>  dssp executable generally gets installed as mkdssp.
>> >
>> > Check if this is the case.
>> >
>> > Regards,
>> >
>> > Sarath
>> >
>> > --
>> > Sarath 

Re: [gmx-users] How to scale epsilon parameters of Lennard-Jones term in .top file?

[Jianguo Li]

To run REST in gmx using lamda-dynamics, you need to edit both ffnonbonded.itp 
and ffbonded.itp. 
In ffnonbonded.itp, you need to define a new atom type corresponding to state 
B, you need to add something like:; name             bond_type       mass       
   charge   ptype  sigma  epsilon 
opls_001_ B      C             6 12.01100 0.500   A    3.75000e-01  
2.19660e-01 ...The charges for state_B can be added in the topology file.For 
bonded parameters you need to rescale the force constants in all sections of 
ffbonded.itp.Finally you also need to edit ions.itp to make sure that the total 
charges for state_B is zero.
Cheers,Jianguo

 On Monday, 8 December 2014, 9:14, 周双艳 zhoush...@lzu.edu.cn wrote:
   

 Hi all,
I am trying to run REST in GROMACS following the way proposed by tsuyoshi 
terakawa. In their method,they implemented REST by rescaling the force-field 
parameters without even changing the code. I have also searched in the mailing 
list and found that we can manipulate the scale parameter in ffnonbonded.itp 
and ffbonded.itp as well as the .rtp file for charges to construct the .top of 
highest temperature which corresponds to lambda=1.Taking the two states(the 
lowest temperature corresponds to lambda=0 regard as state A and highest 
temperature corresponds to lambda=1 regard as state B) into the same .top file, 
and then we can directly use the Hamiltonian REM routine of GROMACS 4,which is 
based on the λ-dynamics and the linear combination potential scheme of the 
two-ends potentials(I do not know whether my understanding is right?).
I add the parameters of state B in to the topology A following the 5.7.4 
Topologies for free energy calculations in GROMACS manual.The bond scaling 
parameters can be added in [bonds] with dA kA dB,kB,where the dA,kA,stand for 
the bond parameters of state A,and the dB,kB stand for the parameters of state 
B.Other scaling parameters such as [angles],[dihedrals] can be treated as the 
same way.My question is how to add the epsilon parameters of Lennard-Jones of 
state B into the .top file? The force field that I used is OPLS-AA force 
field,is it true to add the epsilon value in the [pairs] part? I do not know in 
[pairs] with the format of :ai aj funct c0 c1 c2 c3,what c0,c1,c2 and c3 stands 
for? 
Would you some body give me some suggestions? thanks very much
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.


   
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Errors about dihidral angle type 9 in free energy perturbation

[Jianguo Li]

Dear All,
I am trying to use free energy perturbation module of gromacs to do hamiltonian 
replica exchange using CHARMM27 all-atom force field (with CMAP) - version 2.0

I am using 4.5.4 version of gromacs

according to manual (Table 5.5), it allows to perturb dihedral angles: proper 
dih. multi,  ftp 9, phi and k are allowed under 'F.E.'

I have edited charmm files( ffbonded.itp and also ffnonbonded.itp) for state 
B parameters.
but when I run simulations, it throws following error (for 23 lines):

ERROR 1 [file topol-edited-charmm.top, line 1453]:
  Cannot automatically perturb a torsion with multiple terms to different
  form.
  Please specify perturbed parameters manually for this torsion in your
  topology!


What is the fix for this?
Why gromacs is not recognising the 'state B' parameters?

I also tried to do this with higher version of gromacs (including latest). It 
throws the same error.


Thank you very much for your time. 

Cheers,Jianguo

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] GB parameters for DNA

[Jianguo Li]

Dear everyone,

I would like to simulate a DNA-protein complex using implicit solvent model. 
Anyone has the GB parameters for phosphorus atom?  I searched the mailing list, 
but did not find the answer.

Thanks in advance

Cheers,
Jianguo 
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Hydrogen bond with chlorine

[Jianguo Li]

Hi Dhawal,

One way you can try is to manually change ｔｈｅ name of chloride to oxygen so 
that the g_hbond code can treat the new atom name as acceptors. Just modify 
.gro file, .top file and ions.itp file and get a new tpr file. And use the 
rerun option of mdrun to get a new trajectory.  Then you can calculate the 
hbond using the new trajectory.

Cheers,
Jianguo 






On Monday, 10 February 2014, 17:49, Dhawal Shah dha...@squ.edu.om wrote:
 
HI there,

I have been working on simulations of Urea and Chloride based compounds. In 
order to analyze my results, I am trying to find hydrogen bond between urea and 
chlorine. 

However, I believe, g_hbond only account for O and N atom type hydrogen bonds. 

How can I find number of hydrogen bonds, if it includes chlorine atoms?

Best Regards,
Dhawal 
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pressure based replica exchange

[Jianguo Li]

Thanks Michael and Mark. 
Implementation of the pressure based replica exchange will be useful for 
membrane systems as membranes will be unstable using temperature based replica 
exchange. 
Btw, I noticed there is a recent paper on surface tension replica exchange 
simulations of membranes: 
http://pubs.acs.org/doi/abs/10.1021/ct400445k 
I will wait for the future versions of gromacs, hope it will be implemented 
soon :-)

Cheers 
Jianguo





On Thursday, 12 December 2013, 14:58, Michael Shirts mrshi...@gmail.com wrote:
 
Pressure replica exchange is not in currently. It will be added
eventually (it's not that hard, just takes time, and hasn't been a
priority.).

Note that pressure temperature control with berendsen pressure control
will be 100% wrong.  For pressure replica exchange to work, the
barostat has to give the correct volume fluctuations, and berendsen
does not give correct volume fluctuations.

Of course, that's irrelevant since pressure replica exchange isn't in yet.

The exchange
 criteria is always of the form min(1,exp(-X), where X =
\beta(Delta (beta U) + Delta (beta P V)).  Where P, beta, and U can
vary with state.

What is in is temperature replica exchange with NPT, where beta
changes, but P stays the same.

On Thu, Dec 12, 2013 at 1:40 AM, Jianguo Li ljg...@yahoo.com.sg wrote:
 Thanks very much. As you suggested, making T with small increments such as 
 300.0, 300.0001, 300.0002 ... leads to complaints :-)

 I am trying to do replica exchange at different surface tensions for my 
 membrane system.
 To achieve different surface tensions for different replica, I only changed 
 Pxy, but keep Pz the same for all replica.

 pcoupl          = berendsen
 pcoupltype      = semi-isotropic
 tau_p           = 0.5 0.5
 ref_p           = 1.0 1.0  ; Pxy and Pz
 compressibility = 4.5e-5  4.5e-5

 I noticed that in the manual, the eq (3.141) shows the exchange probability. 
 Can you explain what does the P1 and P2 represent? Pxy or Pz?

 Also, the manual mentioned about using Hamiltonian and temperature replica 
 exchange simultaneously (eq 3.143). But there is no pressure term in the 
 acceptance criteria (eq 3.143). I am wondering if 
 pressure+temperature+Hamiltonian replica exchange has been implemented in 
 Gromacs. If yes, what is the general equation of acceptance criteria?

 Cheers,
 Jianguo







 On Tuesday, 10 December 2013, 17:49, Mark Abraham mark.j.abra...@gmail.com 
 wrote:






 On Tue, Dec 10, 2013 at 1:47 PM, Jianguo Li ljg...@yahoo.com.sg wrote:

 Dear All,

Is it possible to do pressure based replica exchange simulations in gromacs? 
Basically I want to do replica exchange simulations for my membrane system at 
different
 surface tensions. If I just set different pressures in the mpd file, then the 
mdrun will complain systems are all the same, there is nothing to exchange. 
Is there any other parameters I need to set?


 Yes, the implementation is a bit broken, and requires that one of ref-t or 
 lambda varies before it even considers the pressure. If you want T constant 
 and P as the replica control variable, you can can only do that by fooling 
 the implementation by having T vary in tiny increments.

 Mark


Thanks a lot!

Jianguo
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.


 --
 Gromacs Users mailing list

 * Please search the archive at 
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
 mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pressure based replica exchange

[Jianguo Li]

Thanks very much. As you suggested, making T with small increments such as 
300.0, 300.0001, 300.0002 ... leads to complaints :-)

I am trying to do replica exchange at different surface tensions for my 
membrane system.
To achieve different surface tensions for different replica, I only changed 
Pxy, but keep Pz the same for all replica.
pcoupl  = berendsen    
pcoupltype  = semi-isotropic    
tau_p   = 0.5 0.5  
ref_p   = 1.0 1.0  ; Pxy and Pz  
compressibility = 4.5e-5  4.5e-5  

I noticed that in the manual, the eq (3.141) shows the exchange probability. 
Can you explain what does the P1 and P2 represent? Pxy or Pz?  

Also, the manual mentioned about using Hamiltonian and temperature replica 
exchange simultaneously (eq 3.143). But there is no pressure term in the 
acceptance criteria (eq 3.143). I am wondering if 
pressure+temperature+Hamiltonian replica exchange has been implemented in 
Gromacs. If yes, what is the general equation of acceptance criteria? 

Cheers,
Jianguo 







On Tuesday, 10 December 2013, 17:49, Mark Abraham mark.j.abra...@gmail.com 
wrote:
 





On Tue, Dec 10, 2013 at 1:47 PM, Jianguo Li ljg...@yahoo.com.sg wrote:

Dear All,

Is it possible to do pressure based replica exchange simulations in gromacs? 
Basically I want to do replica exchange simulations for my membrane system at 
different surface tensions. If I just set different pressures in the mpd file, 
then the mdrun will complain systems are all the same, there is nothing to 
exchange. Is there any other parameters I need to set?


Yes, the implementation is a bit broken, and requires that one of ref-t or 
lambda varies before it even considers the pressure. If you want T constant and 
P as the replica control variable, you can can only do that by fooling the 
implementation by having T vary in tiny increments.

Mark
 

Thanks a lot!

Jianguo
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.