Re: [gmx-users] Simulating a particle surface for interaction with peptides

[Justin A. Lemkul]

Muhammad Naqvi wrote:

Hi all,
Wonderful community here! FAQs andManuals on one side, nothing beats the advice 
of experts. Whoever started this forum, thank you. I am learning a lot.

I have a question of my own. I am trying to see the interaction of certain 
surfactants and co-surfactants at a hydrophobic interface. To that end I have 
made a gro and top file using the element carbon, minimizing its box size to 
approximately its atomic radius 0.1nm by editconf, concatenating it by genconf 
100 times in x and y directions but only once in z, giving 1 carbon atoms. 
This generates a very nice surface. Then I follow up with editconf again to 
increase the size of the configuration file in the z direction to 10nm as well. 
So the end result is a 10x10x10nm box with a hydrophobic carbon wall on one 
side of the box. The wall's integrity is maintained using position restraints 
of a point for each carbon. To check the correctness of this procedure, I 
performed a minimization, however, during preprocessing using grompp a fatal 
error occurred:
 
Last line read:

'[ molecules ]'
Invalid order for directive molecules

I would like to inquire as to what this error is and how to avoid it. Just to 
verify if the manually produced topology or the configuration files were 
correct, I processed a benzene ring through the same procedure, ending up with 
the same error. Here is the topology file:


#include "ffgmx.itp"

[ moleculetype ]
; Name nrexcl
carbon  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1   C 1  carbon CAN 10.000  12.0350

[ position restraints ]
1 1 1000 1000 1000 ; restrain every carbon atom to a point

[ molecules ]
carbon 1

Any help would be highly appreciated. 



See the manual, Table 5.3 - you're missing the mandatory [system] directive.  If 
you get an "invalid order" error, either something is out of order or missing.


-Justin


Cheers,
Ali


--


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] Simulating a particle surface for interaction with peptides

[Muhammad Naqvi]

Hi all,
Wonderful community here! FAQs andManuals on one side, nothing beats the advice 
of experts. Whoever started this forum, thank you. I am learning a lot.

I have a question of my own. I am trying to see the interaction of certain 
surfactants and co-surfactants at a hydrophobic interface. To that end I have 
made a gro and top file using the element carbon, minimizing its box size to 
approximately its atomic radius 0.1nm by editconf, concatenating it by genconf 
100 times in x and y directions but only once in z, giving 1 carbon atoms. 
This generates a very nice surface. Then I follow up with editconf again to 
increase the size of the configuration file in the z direction to 10nm as well. 
So the end result is a 10x10x10nm box with a hydrophobic carbon wall on one 
side of the box. The wall's integrity is maintained using position restraints 
of a point for each carbon. To check the correctness of this procedure, I 
performed a minimization, however, during preprocessing using grompp a fatal 
error occurred:
 
Last line read:
'[ molecules ]'
Invalid order for directive molecules

I would like to inquire as to what this error is and how to avoid it. Just to 
verify if the manually produced topology or the configuration files were 
correct, I processed a benzene ring through the same procedure, ending up with 
the same error. Here is the topology file:


#include "ffgmx.itp"

[ moleculetype ]
; Name nrexcl
carbon  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1   C 1  carbon CAN 10.000  12.0350

[ position restraints ]
1 1 1000 1000 1000 ; restrain every carbon atom to a point

[ molecules ]
carbon 1

Any help would be highly appreciated. 

Cheers,
Ali
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[gmx-users] making topology file for infinite crystal

[Vishal Agarwal]

Dear All,

Can anyone help me how can I go about preparing the topology file for an
infinite crystal of cellulose. I have prepared the .gro file for 5X5X5 unit
cells of cellulose II using GROMACS utility and intend to apply periodic BC
on it. It has a glucose molecule as building block (GCLA). When I try
running pdbgmx, I get an error for extra hydrogens (which is not there in
itp file but is actually there in the original structure which I am using)
and missing oxygen (-O).


-- 
Regards

***
Vishal Agarwal
Research Scholar
University of Massachusetts, Amherst
***
'Your only obligation in any lifetime is to be true to yourself."
---Richard Bach
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Re: [gmx-users] What is demux.pl script

[Justin A. Lemkul]

zuole wrote:

Dear Justin,
 
Thank you so much for your explaination. But I tried and still can not 
find the demux.pl script. Probably it was the installation problem. If 
you donot mind, would you please send the script to me? Your help is 
sincerely appreciated.
 


That's not a good idea.  If your installation did not work, then providing you 
with a single script is not going to do you much good; likely other things are 
broken, as well.  Further, I don't know what version of Gromacs you're using, 
and there may have been changes to the software.


If you suspect an installation problem, or some other underlying issue, please 
be sure you're following the installation instructions carefully:


http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions

If your installation is not working, please start a new thread with a detailed 
description of what you're doing (exact commands), hardware, compilers used, and 
any relevant error messages.


-Justin


Thanks,
Jackie

 
 > Date: Fri, 5 Feb 2010 21:22:24 -0500

 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] What is demux.pl script
 >
 >
 >
 > zuole wrote:
 > > Hello,
 > >
 > > I've been reading all of the archived questions on the analysis of 
REMD
 > > in Gromacs, and I'm still a bit confused. It appears that the first 
step

 > > is to use the demux.pl script to demultiplex the REMD trajectories.
 > > However, I am unable to find this demux.pl file in
 > > the src/contrib/script/ folder. Can anyone please help me out on 
this? I
 > > would really want to know where to find the script or what the 
content is.

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

 >
 > -Justin
 >
 > > Thanks,
 > >
 > > Jackie
 > >
 > > 


 > > Hotmail: 免费、可靠、丰富的电子邮件服务。 立即获取。
 > > 
 > >
 >
 > --
 > 
 >
 > Justin A. Lemkul
 > Ph.D. Candidate
 > ICTAS Doctoral Scholar
 > MILES-IGERT Trainee
 > Department of Biochemistry
 > Virginia Tech
 > Blacksburg, VA
 > jalemkul[at]vt.edu | (540) 231-9080
 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >
 > 
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--


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

[Bruce D. Ray]

On Sat, February 6, 2010 at 11:08:30 AM, Antoine Delmotte 

wrote:
> Thank you very much for this, Bruce. It will help me, for sure. 
> 
> Could you just let me know where you found the parameters or how you
generated them?

Most of the parameters  came from the entry for threonine in  ffoplsaa.rtp
The remainder came from running the most recent beta test version of
topolbuild 1.3 with the command line

 /usr/local/bin/topolbuild -dir /usr/local/topolbuild -ff oplsaa -n tpo_pep 
-charge
 

which generates an OPLSaa topology with parameters found originally
in the Gromacs OPLSaa installation against a short peptide containing
phosphothreonine and sets the atom charges to the OPLSaa atom type
charges.  I then edited the threonine entry from ffoplsaa.rtp according
to add in the phosphate atom types, and change those atom types that are
altered by the presence of the phosphate.  Finally, I adjusted the charge
on the phosphorous from the charge given in ffoplsaanb.itp in order to
have the total charge come out as -2 for a fully ionized phosphate.
The exact ionization would depend on pH, of course, and I would have
to run the command for protonated TPO (TPH ? or TPH2 ? for the mono-
and di-protonated species?) to further correct atom types and charges.


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



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

[Antoine Delmotte]

Thank you very much Fairuz. I will try this.

Le 6/02/2010 1:20, fairuz zulkifli a écrit :

to create itp file with OPLS force feild, you can try use GAMESS.
-fairuz-



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

[Antoine Delmotte]

Thank you very much for this, Bruce. It will help me, for sure.

Could you just let me know where you found the parameters or how you 
generated them?


Thanks in advance.

Regards,

Antoine

Le 5/02/2010 22:39, Bruce D. Ray a écrit :
On Fri, February 5, 2010 at 1:06:34 PM, Antoine Delmotte 


wrote:
> I would like to simulate the CDK9 protein (3BLH in PDB), but there 
is one residue (TPO,

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

> force fields).
>
> Does anyone have an idea about where I could get the 
phosphothreonine itp file for OPLS

> force field?
>
> Otherwise, could someone give me clues or the link to a good 
tutorial about how to create

> this itp file myself?
>
> Molecular dynamics is something completely new for me so, sorry if I 
ask stupid questions.
> It also seems I am not the first one to have this problem but I 
could not find any solution on

> the archive of the mailing list.

The charges probably need a little more work, but this might be a 
start towards an

rtp file for phosphothreonine to add to ffoplsaa.rtp.

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


I hope that helps.


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




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

[Antoine Delmotte]

Thank you very much for your quick response, Justin. I guess I need a 
little bit more practise to make the parametrization myself. Do you have 
any clues on where I could find published parameters? Are there 
databases for this or something similar?


Regards,

Antoine

Le 5/02/2010 18:23, Justin A. Lemkul a écrit :



Antoine Delmotte wrote:

Dear gmx-users,

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


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


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




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

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




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


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




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


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

-Justin


I thank you in advance.

Best regards,

Antoine




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








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

[Justin A. Lemkul]

Antoine Delmotte wrote:


Thank you very much for your quick response, Justin. I guess I need a 
little bit more practise to make the parametrization myself. Do you have 
any clues on where I could find published parameters? Are there 
databases for this or something similar?




Literature searching is your best bet.  But as far as I know, there is no 
database of previously-published parameters.  Understanding the intrinsics of 
the force field (the original derivation and subsequent improvements) will be 
the most useful for you to understand the intrinsics of the force field.


If you're dead set on using OPLS, then you probably have (a lot) of work cut out 
for you.  Parameters for phosphorylated Ser, Thr, and Tyr for Gromos96 43a1 were 
published some time ago.


-Justin


Regards,

Antoine

Le 5/02/2010 18:23, Justin A. Lemkul a écrit :



Antoine Delmotte wrote:

Dear gmx-users,

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


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


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




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

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




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


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




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


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

-Justin


I thank you in advance.

Best regards,

Antoine




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











--


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


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Re: [gmx-users] SPC model for water, is suitable for amber03 force field?

[Justin A. Lemkul]

shahab shariati wrote:

Dear Justin
 
thanks for your attention
 
therefore, should I use tip3p.itp file from 
http://chemistry.csulb.edu/ffamber/ and spc216.gro from top in gromacs 
program?




Per the link I provided earlier, any equilibrated, 3-point water configuration 
should do the job.  I believe the ffamber ports also contain a file called 
"ffamber_tip3p.gro" that can also be used, if you prefer, but really spc216.gro 
should do the job provided you equilibrate sufficiently with TIP3P parameters.


-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] SPC model for water, is suitable for amber03 force field?

[shahab shariati]

Dear Justin

thanks for your attention

therefore, should I use tip3p.itp file from
http://chemistry.csulb.edu/ffamber/ and spc216.gro from top in gromacs
program?
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Re: [gmx-users] SPC model for water, is suitable for amber03 force field?

[Justin A. Lemkul]

shahab shariati wrote:

Hi all
 
How I can obtain tip3p.itp and tip3p.gro files for amber force field to 
use them in gromacs program for simulation?


You do not need a tip3p.gro, see here:

http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file

 
there are tip3p.itp and tip3p.gro files in top folder of gromacs which 
are suitable for gromacs force fields no amber force fields.




AMBER-specific TIP3P parameter files (and some others) come with the ffamber 
ports:

http://chemistry.csulb.edu/ffamber/

-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] SPC model for water, is suitable for amber03 force field?

[shahab shariati]

Hi all

How I can obtain tip3p.itp and tip3p.gro files for amber force field to use
them in gromacs program for simulation?

there are tip3p.itp and tip3p.gro files in top folder of gromacs which are
suitable for gromacs force fields no amber force fields.
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Re: [gmx-users] Re: general question

[Justin A. Lemkul]

bharat gupta wrote:

Hi all,

This is a general question I wanna ask about deposition of sequences
in NCBI or UNIPROT :-

The sequence that is displayed in NCBI or UNIPROT starts from either
the N terminus or the C- terminus >???



Please remember that this forum is for Gromacs-related questions.  Any basic 
biochemistry textbook will tell you that the convention for protein sequences is 
from N to C.


-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] Re: general question

[bharat gupta]

Hi all,

This is a general question I wanna ask about deposition of sequences
in NCBI or UNIPROT :-

The sequence that is displayed in NCBI or UNIPROT starts from either
the N terminus or the C- terminus >???

-- 
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinformatics
Pondicherry University
Puducherry
India
Mob. +919962670525
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Re: [gmx-users] SPC model for water, is suitable for amber03 force field?

[Justin A. Lemkul]

shahab shariati wrote:

Hi all
 
I am beginner in gromacs.
 
I want to simulate interaction between protein and dna. SPC model for 
water, is suitable for amber03 force field.




The best idea is to do your homework.  Read the paper for the original 
derivation of AMBER03, and any subsequent work that has been done that may have 
used the SPC water model.  Generally, the AMBER force fields are used with 
TIP3P, but that certainly does not preclude the possibility that another model 
may be appropriate.


-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] SPC model for water, is suitable for amber03 force field?

[shahab shariati]

Hi all

I am beginner in gromacs.

I want to simulate interaction between protein and dna. SPC model for water,
is suitable for amber03 force field.
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Re: [gmx-users] -ter in pdb2gmx

[Justin A. Lemkul]

leila karami wrote:

Hi
 
1) what means of option -ter in pdb2gmx command?


The option allows you to set the protonation state.

 
2) I simulate protein-dna complex and I put N and C terminal as NH3+ and 
COO-, respectively for obtaining zwitterionic condition.
 
what is difference between 1 and 2




The difference should be fairly obvious, based on the nomenclature printed by 
pdb2gmx.  For N-termini, choice 1 is NH3+ and 2 is NH2, and analogously for the 
C-terminus.  The default is charged, so if you want charged termini, you don't 
need to be using the -ter flag.


-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] -ter in pdb2gmx

[leila karami]

Hi

1) what means of option -ter in pdb2gmx command?

2) I simulate protein-dna complex and I put N and C terminal as NH3+ and
COO-, respectively for obtaining zwitterionic condition.

what is difference between 1 and 2
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[gmx-users] residence time and life time of hydrogen bond

[leila karami]

Hi

What is difference between residence time and life time of hydrogen bond?

Theses two parameters are obtained by command g_hbond.

is my opinion true? how?
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Re: [gmx-users] Distance restraint energy terms

[Justin A. Lemkul]

nikhil damle wrote:

Hi,

I have applied distance restraints on my system during MD simulation 
through following options:

"disre = simple" and disre_fc = 2000 in .mdp file.
Now i wish to see the energy term corresponding to these restraints in 
principle to be written in .edr file. But g_energy programme does not 
list any term corresponding to these restraints.




Then you haven't applied any distance restraints.


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



Setting distance restraints isn't as simple as setting some .mdp options, you 
have to have a [distance_restraints] section in the topology that describes 
exactly what those restraints are.  This is all in the manual, and has been 
discussed a number of times on the list, so there should also be some pointers 
in the archives.


If it works, you should see the corresponding energy term.

-Justin


Plz help ASAP

Regards,
Nikhil



The INTERNET now has a personality. YOURS! See your Yahoo! Homepage 
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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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