Re: [gmx-users] Adding external magnetic filed to GROMACS

[Sam Dav]

Thank you Alex,
I need to know how to edit the source code to generate the magnetic force.
the question is how I can edit it?
Thanks

On Fri, Mar 24, 2017 at 1:54 PM, Alex  wrote:

> There are no magnetic fields in Gromacs, unless you are willing to edit
> the source code and generate forces arising from it.
>
> Alex
>
>
>
> On 3/24/2017 12:47 PM, Sam Dav wrote:
>
>> Hello all,
>> I'm new user and I have done some simulations. Now, I'm trying to use an
>> external magnetic field and I found its not implemented such as electric
>> field. Does anyone know how to add it and which filed I should modify?.
>> Thank you in advance
>> Sam
>>
>
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Re: [gmx-users] Adding external magnetic filed to GROMACS

[Alex]

There are no magnetic fields in Gromacs, unless you are willing to edit 
the source code and generate forces arising from it.


Alex


On 3/24/2017 12:47 PM, Sam Dav wrote:

Hello all,
I'm new user and I have done some simulations. Now, I'm trying to use an
external magnetic field and I found its not implemented such as electric
field. Does anyone know how to add it and which filed I should modify?.
Thank you in advance
Sam


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[gmx-users] Adding external magnetic filed to GROMACS

[Sam Dav]

Hello all,
I'm new user and I have done some simulations. Now, I'm trying to use an
external magnetic field and I found its not implemented such as electric
field. Does anyone know how to add it and which filed I should modify?.
Thank you in advance
Sam
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[gmx-users] Clarification for the meaning of ncoords in GROMACS 5.0.4 pull code

[Sajeewa Pemasinghe]

Hi,

I have two molecules which are not moving in the z axis due to being
continuous across the periodic boxes. I want to keep the distance between
them fixed by pulling along x and y axes. So as I am pulling along x and y
axes does my ncoords = 2 ?  By going along with this logic as long as my
pull-geometry = distance, will the maximum number for ncoords be 3 (i.e.
pulling along all x, y , and z axes)? I really appreciate an explanation.

Thank you very much

Sajeewa Dewage
New York University - Abu Dhabi
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[gmx-users] membed software inconsistency error

[Jason Mast]

Dear Gromacs Users,

I'm trying to embed a protein into a lipid bilayer using the -membed option
of gmx mdrun. After executing the command:
gmx mdrun -s topol.tpr -deffnm out -membed embed.dat -mp topol.top -mn
index.ndx
I select the groups for the Protein and Lipid_Bilayer when prompted for
them, and then I get an error message:

Program: gmx mdrun, version 2016
Source file: src/gromacs/topology/mtop_util.cpp (line 249)

Software inconsistency error:
gmx_mtop_atomlookup_settle_init called without settles

I have tried searching online via Google for the meaning and solution to
this error, but all I can find are links to the source code that contains
that method call. Section 6.14 of the Gromacs User Manual doesn't contain
any information to address this error. Additionally this error isn't listed
at www.gromacs.org/Documentation/Errors.

I have tried this with and without the -mp and -mn options, and I receive
the same response. I have checked all of the input files (system.gro,
index.ndx, topol.top, embed.mdp, & embed.dat) for errors, and everything
looks correct.

Before executing mdrun I run gmx grompp and it completes without any
warnings or errors. It produces a few common notes, which I consider to be
okay and not relevant to this error.

Here is a subset of the mdp parameters which could potentially be relevant:
comm-mode   = Linear
comm-grps = System
cutoff-scheme = group ; Verlet is not yet implemented for use with membed
tcouple   = v-rescale
tc-groups= Protein Lipid_Bilayer Water
Pcoupl= no
freezegrps   = Protein
freezedim= Y Y Y
energygrps   = Protein
energygrp_excl = Protein Protein

I am using the Martini 2.2 coarse grain force field. I have used this force
field for other md simulations without using the membed tool, and this
error was never produced.

Can anyone offer any guidance or pointers about what I could be doing wrong
or otherwise a way work around the error?

Thank you for reading,
Jason
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Re: [gmx-users] Pull code grompp error

[Souparno Adhikary]

Hi Kausar,

I tried it with an index file. It seemed to run fine but did not produce
any "pull" i.e. shifting away of the DNA molecule from the protein. I used
a harmonic potential. And also, why do I need to specify the index file
when, according to the error itself, it can be run without making an index
file, just putting the name of the molecules?

Thanks,

Souparno

On Fri, Mar 24, 2017 at 1:03 PM, Tasneem Kausar 
wrote:

> Define you pull group in index file  as the error message says.
>
> On Fri, Mar 24, 2017 at 12:18 PM, Souparno Adhikary  >
> wrote:
>
> > Hi,
> >
> > Below is my .mdp code for pulling as found in the tutorial by Justin
> > Lemkul. I made the required changes to match my version syntax.
> >
> > pull= umbrella
> > pull_ngroups= 2
> > pull_group0= Protein_chain_A
> > pull_group1= DNA_chain_B
> > pull_group2= DNA_chain_C
> > pull_geometry= distance  ; simple distance increase
> > pull_dim = Y N N
> > pull_rate1= 0.01  ; 0.01 nm per ps = 10 nm per ns
> > pull_rate2= 0.01
> > pull_k1   = 1000  ; kJ mol^-1 nm^-2
> > pull_k2   = 1000
> > pull_start   = yes   ; define initial COM distance > 0
> >
> > When I tried to grompp using this code, it generates an error:
> >
> > Fatal error:
> > Group topol_Protein_chain_A referenced in the .mdp file was not found in
> > the index file.
> > Group names must match either [moleculetype] names or custom index group
> > names, in which case you must supply an index file to the '-n' option
> > of grompp.
> >
> > I searched for the solutions in the Gromacs forum and found it might be
> due
> > to name mismatch. But, in my case, the names are exactly same as
> referenced
> > in the *.mdp file. Below is the molecule names from the topol.top file.
> >
> > [ molecules ]
> > ; Compound#mols
> > Protein_chain_A 1
> > DNA_chain_B 1
> > DNA_chain_C 1
> > SOL 33542
> > NA   125
> > CL   98
> >
> > Can you please help to solve the problem? I tried with changing the names
> > to Protein and DNA (the residue types) and changing the ngroups to 3.
> > Nothing worked.
> >
> > Regards,
> >
> > Souparno Adhikary
> > University of Calcutta,
> > India.
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Re: [gmx-users] COMMAND IN HBOND

[Neha Gupta]

Hi,


Thank you for the reply.

Actually, we get the number of hydrogen bonds in .xvg file using

gmx hbond -s prd.tpr -f prd.xtc -n index.ndx -num hbnum.xvg
.

Can we generate an output file similar to that, which prints the bonding
residues of protein and ligand?


Thanks,
Neha



On Fri, Mar 24, 2017 at 8:05 PM, Erik Marklund 
wrote:

> Dear Neha,
>
> Gromacs doesn’t offer that much in terms of viewing. This sounds more like
> a PyMol/VMD/Other question.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se
>
> On 24 Mar 2017, at 14:33, Neha Gupta > wrote:
>
> Hi gromacs users,
>
> What is the command to view the residues of protein and atoms of ligand
> involved in hydrogen bond?
>
> Thanks,
> Neha
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Re: [gmx-users] COMMAND IN HBOND

[Erik Marklund]

Dear Neha,

Gromacs doesn’t offer that much in terms of viewing. This sounds more like a 
PyMol/VMD/Other question.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 24 Mar 2017, at 14:33, Neha Gupta 
> wrote:

Hi gromacs users,

What is the command to view the residues of protein and atoms of ligand
involved in hydrogen bond?

Thanks,
Neha
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[gmx-users] COMMAND IN HBOND

[Neha Gupta]

Hi gromacs users,

What is the command to view the residues of protein and atoms of ligand
involved in hydrogen bond?

Thanks,
Neha
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Re: [gmx-users] FSync error

[Souparno Adhikary]

Hi Mark,

I understand it's prehistoric. But, I would be happier if somebody makes
understand the system admins at the CDAC-BRAF that their version is
prehistoric.

The problem has not been solved yet. I'm running the simulation in parts
reading from the checkpoint files. Will that be too risky for the results?

Regards,

Souparno.

On 24 Mar 2017 16:22, "Mark Abraham"  wrote:

> Hi,
>
> Mdrun can't access that file properly, but there's no real way for it to
> understand why. A network file system could disappear and mdrun can't know
> that. By the way, 4.5.6 is prehistoric - please update for faster
> simulations, more chance of people being able to help you, and fewer bugs!
>
> Mark
>
> On Fri, 24 Mar 2017 09:34 Souparno Adhikary  wrote:
>
> > I'm getting the following error in a 500ps pull code simulation. I
> checked
> > out the forum for probable solve and it says it might be due to disk
> space
> > usage or permission. In my case, I have enough disk quota left and I have
> > permission to write in the directory. Can you please help?
> >
> > Usual MD simulations run fine. The error comes only when the pull code is
> > applied.
> >
> > Error:
> >
> > ---
> > Program mdrun_mpi, VERSION 4.5.6
> > Source code file: checkpoint.c, line: 1287
> >
> > File input/output error:
> > Cannot fsync 'tp_pull.xvg'; maybe you are out of disk space?
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > ---
> >
> > Attached is my mdp file for the pull code. Framed broadly on Justin
> > Lemkul's tutorial *.mdp file.
> >
> > Can you please help to indicate what might be the problem?
> >
> > Thanks,
> >
> > Souparno Adhikary,
> > University of Calcutta,
> > India
> > --
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Re: [gmx-users] Getting charges of the system out of the simulation in human-readable form

[Mark Abraham]

Hi,

On Fri, 24 Mar 2017 11:25 Marko Sever  wrote:

So my question is, what is the most simple way to get a file with residue
and atom types in addition to charges out of the files created at the end
of the simulation?


There isn't one apart from what is written by eg gmx editconf -s your.tpr
-o a.pdb or similar. That is a very verbose and redundant representation.
The tree-like structure of the .top and .tpr file is more useful for
everything except "what is the type of atom 2948" etc.

The return question is "Why is it more suitable to have the tree fully
written out on order to make such queries?"

I tried dumping the .tpr file but its file structure is a bit too
complicated, I'd preffer something easier. Also since I created the input
files with Charmm-gui I got a lot of .itp files, but I would preffer to
have just one?


The separate files make re-use in different simulations easier to manage.
Why is one file more useful?

Also if I make again a new pdb of the system and go with gmx pdb2gmx ->
"gmx pdb2gmx -f mdforpsf.pdb -o prcs.gro -ff charmm36chol_psm_dopc -water
tip3p" it errors out with the following error:


Program gmx pdb2gmx, VERSION 5.1.2
Source code file:
/share/apps/gromacs/5.1.2/gromacs-5.1.2/src/gromacs/gmxpreprocess/resall.c,
line: 645

Fatal error:
Residue 'PSM' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


While PSM.itp is located in the charmm36chol_psm_dopc.ff folder, and other
many itp files get read fine...weird...


Charmm gui and pdb2gmx do the same job as each other: producing itp files.
Pdb2gmx is complaining about missing rtp files, which nothing has provided.

Mark

Thanks for the help!
Marko
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Re: [gmx-users] FSync error

[Mark Abraham]

Hi,

Mdrun can't access that file properly, but there's no real way for it to
understand why. A network file system could disappear and mdrun can't know
that. By the way, 4.5.6 is prehistoric - please update for faster
simulations, more chance of people being able to help you, and fewer bugs!

Mark

On Fri, 24 Mar 2017 09:34 Souparno Adhikary  wrote:

> I'm getting the following error in a 500ps pull code simulation. I checked
> out the forum for probable solve and it says it might be due to disk space
> usage or permission. In my case, I have enough disk quota left and I have
> permission to write in the directory. Can you please help?
>
> Usual MD simulations run fine. The error comes only when the pull code is
> applied.
>
> Error:
>
> ---
> Program mdrun_mpi, VERSION 4.5.6
> Source code file: checkpoint.c, line: 1287
>
> File input/output error:
> Cannot fsync 'tp_pull.xvg'; maybe you are out of disk space?
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> Attached is my mdp file for the pull code. Framed broadly on Justin
> Lemkul's tutorial *.mdp file.
>
> Can you please help to indicate what might be the problem?
>
> Thanks,
>
> Souparno Adhikary,
> University of Calcutta,
> India
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[gmx-users] Getting charges of the system out of the simulation in human-readable form

[Marko Sever]

So my question is, what is the most simple way to get a file with residue and 
atom types in addition to charges out of the files created at the end of the 
simulation?
I tried dumping the .tpr file but its file structure is a bit too complicated, 
I'd preffer something easier. Also since I created the input files with 
Charmm-gui I got a lot of .itp files, but I would preffer to have just one?

Also if I make again a new pdb of the system and go with gmx pdb2gmx -> "gmx 
pdb2gmx -f mdforpsf.pdb -o prcs.gro -ff charmm36chol_psm_dopc -water tip3p" it 
errors out with the following error:


Program gmx pdb2gmx, VERSION 5.1.2
Source code file: 
/share/apps/gromacs/5.1.2/gromacs-5.1.2/src/gromacs/gmxpreprocess/resall.c, 
line: 645

Fatal error:
Residue 'PSM' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


While PSM.itp is located in the charmm36chol_psm_dopc.ff folder, and other many 
itp files get read fine...weird...

Thanks for the help!
Marko
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Re: [gmx-users] Regarding structure

[Dilip H N]

I am sorry..



   Sent with Mailtrack


On Fri, Mar 24, 2017 at 9:44 AM, Jonathan Saboury  wrote:

> Please be considerate to others and only post a topic once. Not only does
> multiple posts annoy others but it greatly diminishes your chances of
> receiving help.
>
> I unfortunately do not have the expertize to help you, but I'm sure someone
> will soon.
>
> - Jonathan
>
> On Thu, Mar 23, 2017 at 9:08 PM, Dilip H N 
> wrote:
>
> > Hello,
> > The glycine .pdb that i have is a non zwitter ionic form, and from this
> if
> > i want to create a topology file from the following command as -
> > gmx pdb2gmx -f gly.pdb -o gly.gro
> > and selected charmm FF i am getting the following msg...
> >
> > Processing chain 1 'A' (10 atoms, 1 residues)
> > Identified residue GLY1 as a starting terminus.
> > Identified residue GLY1 as a ending terminus.
> > 8 out of 8 lines of specbond.dat converted successfully
> > Start terminus GLY-1: GLY-NH3+
> > End terminus GLY-1: COO-
> >
> > It is showing tht glycine as zwitterionic form, But i dnt want it to be
> in
> > zwitterionic form... How can i solve this issue..??
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Research Scholar,
> > Department of Chemistry, NITK.
> >
> >
> >
> >    Sent with Mailtrack
> >  > referral=cy16f01.di...@nitk.edu.in=22>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
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With Best Regards,

DILIP.H.N
Research Scholar,
Department of Chemistry, NITK.
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Re: [gmx-users] Analysis pull code simulation data to obtain Strain Stress curve

[Alex]

Hi there,

Everyone is confused about how to get stress-strain curves from Justin's 
tutorial. Because it has nothing to do with nanomechanics. Obtaining 
Young's modulus from a particle-based simulation is quite elementary, if 
a clear physical picture is present.


Please describe your system and explain what you are trying to achieve.

Alex


On 3/24/2017 2:15 AM, Md. Imrul Reza Shishir wrote:

Dear all
My target is to calculate nanomechanical properties (i.e. young's
modulus/elastic modulus) from a strain-stress curve.
For this purpose, I study Beven lab umbrella sampling pull code simulation.
After that, I also run the same procedure simulation on my desire system.
But I am now confused how I can obtain strain-stress curve from this
simulation data.

I want some guidance about this purpose.

Thank you very much



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[gmx-users] FSync error

[Souparno Adhikary]

I'm getting the following error in a 500ps pull code simulation. I checked
out the forum for probable solve and it says it might be due to disk space
usage or permission. In my case, I have enough disk quota left and I have
permission to write in the directory. Can you please help?

Usual MD simulations run fine. The error comes only when the pull code is
applied.

Error:

---
Program mdrun_mpi, VERSION 4.5.6
Source code file: checkpoint.c, line: 1287

File input/output error:
Cannot fsync 'tp_pull.xvg'; maybe you are out of disk space?
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Attached is my mdp file for the pull code. Framed broadly on Justin
Lemkul's tutorial *.mdp file.

Can you please help to indicate what might be the problem?

Thanks,

Souparno Adhikary,
University of Calcutta,
India
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[gmx-users] Analysis pull code simulation data to obtain Strain Stress curve

[Md. Imrul Reza Shishir]

Dear all
My target is to calculate nanomechanical properties (i.e. young's
modulus/elastic modulus) from a strain-stress curve.
For this purpose, I study Beven lab umbrella sampling pull code simulation.
After that, I also run the same procedure simulation on my desire system.
But I am now confused how I can obtain strain-stress curve from this
simulation data.

I want some guidance about this purpose.

Thank you very much

-- 
*Md Imrul Reza Shishir*
Master Student
*Inha University*
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Re: [gmx-users] Pull code grompp error

[Tasneem Kausar]

Define you pull group in index file  as the error message says.

On Fri, Mar 24, 2017 at 12:18 PM, Souparno Adhikary 
wrote:

> Hi,
>
> Below is my .mdp code for pulling as found in the tutorial by Justin
> Lemkul. I made the required changes to match my version syntax.
>
> pull= umbrella
> pull_ngroups= 2
> pull_group0= Protein_chain_A
> pull_group1= DNA_chain_B
> pull_group2= DNA_chain_C
> pull_geometry= distance  ; simple distance increase
> pull_dim = Y N N
> pull_rate1= 0.01  ; 0.01 nm per ps = 10 nm per ns
> pull_rate2= 0.01
> pull_k1   = 1000  ; kJ mol^-1 nm^-2
> pull_k2   = 1000
> pull_start   = yes   ; define initial COM distance > 0
>
> When I tried to grompp using this code, it generates an error:
>
> Fatal error:
> Group topol_Protein_chain_A referenced in the .mdp file was not found in
> the index file.
> Group names must match either [moleculetype] names or custom index group
> names, in which case you must supply an index file to the '-n' option
> of grompp.
>
> I searched for the solutions in the Gromacs forum and found it might be due
> to name mismatch. But, in my case, the names are exactly same as referenced
> in the *.mdp file. Below is the molecule names from the topol.top file.
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_A 1
> DNA_chain_B 1
> DNA_chain_C 1
> SOL 33542
> NA   125
> CL   98
>
> Can you please help to solve the problem? I tried with changing the names
> to Protein and DNA (the residue types) and changing the ngroups to 3.
> Nothing worked.
>
> Regards,
>
> Souparno Adhikary
> University of Calcutta,
> India.
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Re: [gmx-users] Regarding structure

[Vytautas Rakeviius]

If you interested in just one glycine one possible solution is to prepare it 
with acpype instead. It respects your hydrogens and you can set charge as 
command line option.
 

On Friday, March 24, 2017 6:14 AM, Jonathan Saboury  
wrote:
 

 Please be considerate to others and only post a topic once. Not only does
multiple posts annoy others but it greatly diminishes your chances of
receiving help.

I unfortunately do not have the expertize to help you, but I'm sure someone
will soon.

- Jonathan

On Thu, Mar 23, 2017 at 9:08 PM, Dilip H N 
wrote:

> Hello,
> The glycine .pdb that i have is a non zwitter ionic form, and from this if
> i want to create a topology file from the following command as -
> gmx pdb2gmx -f gly.pdb -o gly.gro
> and selected charmm FF i am getting the following msg...
>
> Processing chain 1 'A' (10 atoms, 1 residues)
> Identified residue GLY1 as a starting terminus.
> Identified residue GLY1 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Start terminus GLY-1: GLY-NH3+
> End terminus GLY-1: COO-
>
> It is showing tht glycine as zwitterionic form, But i dnt want it to be in
> zwitterionic form... How can i solve this issue..??
>
> --
> With Best Regards,
>
> DILIP.H.N
> Research Scholar,
> Department of Chemistry, NITK.
>
>
>
>   Sent with Mailtrack
>  referral=cy16f01.di...@nitk.edu.in=22>
> --
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>
> * Please search the archive at http://www.gromacs.org/
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[gmx-users] Pull code grompp error

[Souparno Adhikary]

Hi,

Below is my .mdp code for pulling as found in the tutorial by Justin
Lemkul. I made the required changes to match my version syntax.

pull= umbrella
pull_ngroups= 2
pull_group0= Protein_chain_A
pull_group1= DNA_chain_B
pull_group2= DNA_chain_C
pull_geometry= distance  ; simple distance increase
pull_dim = Y N N
pull_rate1= 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_rate2= 0.01
pull_k1   = 1000  ; kJ mol^-1 nm^-2
pull_k2   = 1000
pull_start   = yes   ; define initial COM distance > 0

When I tried to grompp using this code, it generates an error:

Fatal error:
Group topol_Protein_chain_A referenced in the .mdp file was not found in
the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

I searched for the solutions in the Gromacs forum and found it might be due
to name mismatch. But, in my case, the names are exactly same as referenced
in the *.mdp file. Below is the molecule names from the topol.top file.

[ molecules ]
; Compound#mols
Protein_chain_A 1
DNA_chain_B 1
DNA_chain_C 1
SOL 33542
NA   125
CL   98

Can you please help to solve the problem? I tried with changing the names
to Protein and DNA (the residue types) and changing the ngroups to 3.
Nothing worked.

Regards,

Souparno Adhikary
University of Calcutta,
India.
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