Re: [gmx-users] how to select head groups of lipid within 10 angstrom of protein

[Peter Stern]

You are probably causing your command to run in the background with “&”.  Try 
using “and” instead.  

Peter

Sent from my iPhone

> On Oct 25, 2019, at 11:45 AM, SHAHEE ISLAM  wrote:
> 
> Hi,
> I am trying to calculate the angle between P and N vector of my lipid
> (popc+popg) with regards to the z axis to see how the protein is affecting
> the membrane. I am using this command, but it does not working
> gmx select -f *.xtc -s *.tpr -select POPG & name P* N* within 1.0 of
> Protein -oi number.dat
> but the problem is, when the command is running only
>  gmx select -f *.xtc -s *.tpr -select POPG
> this command.
> Can anyone please guide me what i am doing wrong.
> Thanking you
> Shahee
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Re: [gmx-users] Transference of dihedral potentials between united atom and all-atom force fields

[Peter Stern]

No, of course not.  United atom potentials are optimized taking into account 
that the hydrogens are not included.  Think about it.  If you use the United 
atom dihedral potential in an all-atom force field you will also be adding to 
that all the dihedral potentials which include the hydrogen atoms.  Clearly 
this is not going to be the same for a particular C-C bond.

And in general, you cannot transfer parameters from one force field to another. 
 I think that has been emphasized repeatedly in this forum.

Regards,
Peter


Sent from my iPhone

On Jun 29, 2019, at 2:10 PM, Pragati Sharma 
mailto:pragati2...@gmail.com>> wrote:

Hello gromacs users,

I have a query regarding transference of dihedral potentials between united
atom and all-atom force fields. Suppose, for a dihedral of four carbon
atoms in polybutadine (united atoms: CH2-CH=CH-CH2). Can I use the same
dihedral potentials or force constants for the same set of atoms in an
all-atom force field where carbon and hydrogens are treated separately
while keeping the potential functions same.

Thanks, Pragati
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Re: [gmx-users] Grompp not producing tpr files

[Peter Stern]

A segmentation fault is a “crash” not a normal exit.  The only information you 
have there is where the program got to before it crashed.  No log file?

Peter

Sent from my iPhone

> On Jun 13, 2019, at 6:04 PM, Israel Estrada  wrote:
> 
> Thanks for the replies!
> 
> Mark, the process seemed to "finish" properly (my terminal did not close, and 
> the command line was waiting for the next command as if it ran normally). I 
> looked for the output file (ions.tpr) in the working directory, or any new 
> files, but nothing was generated.
> 
> Bratin, here is what my terminal displayed,
> "command line:
> gmx grompp -f ions.mdp -c box.gro -o ions.tpr -p topol.top
> 
> Setting the LD random seed to 973096069
> Segmentation fault (core dumped)"
> The last part seems to be the error, right?
> 
> Thanks again!!
> -Israel
> 
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Bratin Kumar 
> Das <177cy500.bra...@nitk.edu.in>
> Sent: Wednesday, June 12, 2019 7:00:55 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Grompp not producing tpr files
> 
> Hi
>   Give here the full error
> 
>> On Thu 13 Jun, 2019, 1:35 AM Mark Abraham,  wrote:
>> 
>> Hi,
>> 
>> Was grompp exiting normally, or crashing? Are you looking in the right
>> place, for a file of the right name? :-)
>> 
>> Mark
>> 
>>> On Wed., 12 Jun. 2019, 18:42 Israel Estrada,  wrote:
>>> 
>>> Hello users,
>>> 
>>> 
>>> I'm running into problems trying to grompp; I'm using the command
>>> 
>>> 
>>> gmx grompp -f ions.mdp -c etc_box.gro  -o ions.tpr -p topol.top
>>> 
>>> 
>>> and the process shows no error messages, but output files are not being
>>> generated. I'm running this on a small molecule, about 20 atoms, with the
>>> hopes that I can modify OPLS parameters as needed. I'm sure the problem
>> is
>>> related to an error in the topology files, but I don't know how or if I
>> can
>>> fix this.
>>> 
>>> 
>>> Any help would be greatly appreciated, thank you!
>>> 
>>> -Israel
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Re: [gmx-users] Force field parameters not known

[Peter Stern]

Hi,

It seems that you typed "cp-r" (no space) instead of "cp -r" (space between cp 
and -r).
"cp" is a Linux command, not Gromacs and as such, anything that starts with a 
"-" is part of a flag or option to the command.
There may be several such flags and they are space delimited.

Regards,
Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Matthew 
Stoodley
Sent: Thursday, February 21, 2019 12:59 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Force field parameters not known

Hi,
I am currently trying to perform a simulation on a chemical molecular machine 
but whenever I try and do the pdb2gmx command and select a force field it comes 
up with the message 'the residue DVHY is not recognised'. From my understanding 
what I should do is to update the residue in the specific force field that I 
want to use. I have tried using the command line: 

cp-r $GMXLIB/residuetypes.dat  $GMXLIB/amber99sb.ff

as it says to use this on the gromacs website but it says the command is not 
recognised. I am using GROMACS 5.0.4.
Any help would be appreciated.Thanks,Matthew
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Re: [gmx-users] How to install a new force-field?

[Peter Stern]

Hi,

Check:

$GMXLIB/share/gromacs/top

Sent from my iPhone

> On Dec 23, 2018, at 20:16, ZHANG Cheng <272699...@qq.com> wrote:
> 
> Hi Justin,
> 
> 
> I can use the new force field if I put it under the working directory.
> 
> 
> You also mentioned that I can put it under $GMXLIB. However, I could not find 
> it when the ff is put at
> /home/lanselibai/Cheng/gromacs-2018.1/build/src/gromacs/gmxlib/charmm36-nov2018.ff
> 
> 
> So what is the directory of $GMXLIB?
> 
> 
> Thank you.
> 
> 
> Cheng
> 
> 
> 
> 
> -- Original --
> From:  "ZHANG Cheng"<272699...@qq.com>;
> Date:  Sun, Dec 23, 2018 11:01 PM
> To:  "gromacs.org_gmx-users";
> 
> Subject:  Re: Re:  How to install a new force-field?
> 
> 
> 
> Thank you very much! I got it now!
> 
> 
> Cheng
> 
> 
> 
> 
> -- Original --
> From:  "ZHANG Cheng"<272699...@qq.com>;
> Date:  Sun, Dec 23, 2018 10:54 PM
> To:  "gromacs.org_gmx-users";
> 
> Subject:  Re: How to install a new force-field?
> 
> 
> 
> Thank you Justin. Do you know how to use the "define = -DUSE_OLD_C36" as 
> shown on 
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
> 
> 
> I want to make sure the CHARMM36m is used instead of CHARMM36.
> 
> 
> 
> 
> 
> 
> -- Original --
> From:  "ZHANG Cheng"<272699...@qq.com>;
> Date:  Sun, Dec 23, 2018 10:38 PM
> To:  "gromacs.org_gmx-users";
> 
> Subject:  How to install a new force-field?
> 
> 
> 
> Dear Gromacs users,
> 
> 
> In the pdb2gmx command, we are asked to select the force field to simulate 
> our protein system. I am told that a99SB-disp and CHARMM36m are better 
> force-field for the proteins. But both of them are not the default ones. Can 
> I ask
> 
> 
> 1) What is the latest officical website to download them?
> At this website,
> http://www.gromacs.org/Downloads/User_contributions/Force_fields
> I could not find a99SB-disp and CHARMM36m.
> 
> 
> 2) How to install them?
> Is there a step-by-step instruction for the installation?
> 
> 
> Thank you.
> 
> 
> Yours sincerely
> Cheng
> 
> 
> CHARMM36m: an improved force field for folded and intrinsically disordered 
> proteins
> https://www.nature.com/articles/nmeth.4067
> 
> 
> a99SB-disp:
> Developing a molecular dynamics force field for both folded and disordered 
> protein states
> https://www.pnas.org/content/115/21/E4758
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Re: [gmx-users] Specifying more than one index group via the command line

[Peter Stern]

Hi,

This is really a linux and not a gromacs question.  There are many ways of 
inputting data to a script depending upon which shell you use.
One way is to input the data from a file.  
You should google how to do this for the shell you use (bash, tcsh, etc.) and 
choose the solution which suits you.

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Francisco Lobo 
Cabrera
Sent: Tuesday, October 23, 2018 10:24 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Specifying more than one index group via the command line

Hello:

Is it possible to specify several index groups through the command line?

For example, to compute hydrogen bonds, hbond needs two index groups. This can 
be done through the interactive prompt, but I need to submit this instruction 
wtih a script. I have searched around but have not found anything.

Thank you for your attention.

Francisco
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Re: [gmx-users] DNA strands are separated

[Peter Stern]

Hi,

This is probably just a periodic boundary issue.  Use gmx trjconv with the -pbc 
nojump option to get both strands of dna in the same box.

Regards,
Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of 
sp...@iacs.res.in
Sent: Tuesday, April 24, 2018 9:23 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] DNA strands are separated

Hii all
I am trying to do DNA simulation in water. I have done 200ns mdrun for that. 
When I am trying to see the snapshot of different frames in VMD, it shows that 
DNA strands are separated and one strand is out of the box. So I couldn't get 
the picture of different frames with actual solvent orientation around the DNA. 
How to solve this problem?

Thanks
sunipa
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Re: [gmx-users] what is the difference between gmx mdrun and gmx tune_pme

[Peter Stern]

http://manual.gromacs.org/programs/gmx-tune_pme.html


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Vidya R
Sent: Friday, September 15, 2017 6:42 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] what is the difference between gmx mdrun and gmx tune_pme

Hi gromacs users,

What is the difference between gmx mdrun and gmx tune_pme? Which is better to 
use in a cluster (especially when we submit our jobs through qsub
command?)




Also, what is the purpose of -np option in gmx tune_pme? Can someone elucidate?


Thanks,
Viday.R
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Re: [gmx-users] pdb2gmx

[Peter Stern]

Is your first residue GLY-12?
If so you have exactly 368 residues in your protein: 12-379

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of ?farial 
tavakoli? ??
Sent: Thursday, July 20, 2017 3:07 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] pdb2gmx

Hello
 I want to create a .gro and .top file from my protein that contains 379 
aminoacids in it's .pdb file by using gromos96 54a7 force field:
pdb2gmx -f protein.pdb -o protein.gro -water spce -ignh but when gro and 
topology files are created , I see that message:
Start terminus GLY-12: GLY-NH3+
End terminus PRO-379: COO-
Checking for duplicate atoms
Generating any missing hydrogen atoms and/or adding termini.
Now there are 368 residues with 3856 atoms Making bonds...
Number of bonds was 3938, now 3933
Generating angles, dihedrals and pairs...
Before cleaning: 6090 pairs
Before cleaning: 8285 dihedrals
Making cmap torsions...There are 2746 dihedrals, 2028 impropers, 5756 angles
  6090 pairs, 3933 bonds and 0 virtual sites Total mass 
42175.307 a.m.u.
Total charge -0.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.46#

Writing coordinate file...

Back Off! I just backed up HDAC2.gro to ./#HDAC2.gro.1#
        - PLEASE NOTE  You have successfully generated a 
topology from: HDAC2.pdb.
The Gromos54a7 force field and the spce water model are used.
        - ETON ESAELP 

However, i ignored this message and continued to use grompp gmx grompp -f 
em.mdp -c solv.gro -p topol.top -o ions.tpr

but faced to this message:
  gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.29# Setting the LD random 
seed to -1863558486 Generated 168 of the 1653 non-bonded parameter combinations 
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'
Removing all charge groups because cutoff-scheme=Verlet Analysing residue names:
There are:   368    Protein residues
There are: 11240  Water residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 79005.00 Calculating 
fourier grid dimensions for X Y Z Using a fourier grid of 72x72x72, spacing 
0.114 0.114 0.114 Estimate for the relative computational load of the PME mesh 
part: 0.10 This run will generate roughly 3 Mb of data

Back Off! I just backed up ions.tpr to ./#ions.tpr.36#


Is there anyone to help me? Why pdb2gmx didnt consider all 379 amino acids of 
my protein and why GOMACS excluded 3 bonded neighours of the protein and 
SOL?and would you please tell what ' removing all charge groups because 
cutoff-scheme=Verlet ' means ? I t means the system is neutral ?

thanks in advanceFarial


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Re: [gmx-users] Displacement of coordinates by an order of magnitude by pdb2gmx

[Peter Stern]

The pdb file is in Angstroms.  Gromacs uses nanometers, thus the decrease by a 
factor of 10 -> 1nm = 10A

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Anna 
Lohning
Sent: Friday, July 07, 2017 6:07 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Displacement of coordinates by an order of magnitude by 
pdb2gmx

Hi
I've looked all through the GROMACS documentation re actions of the PDB2GMX 
command but I cant' see a reference to why it appears to change the coordinates 
of the input .pdb file (basically decreasing them by an order of magnitude). Is 
this normal? When grepping out your docked ligands this causes problems later 
when you put the ligand coordinates back in prior to creating the box, having 
to then alter those coordinates in the same manner. I am obviously missing some 
important information!  (I using Gromacs 5.0.4) Kind regards & many thanks/Anna


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Re: [gmx-users] NMA eigenvectors doubts

[Peter Stern]

How many protein atoms do you have?  How many eigenvectors?  The program is not 
going to calculate the normal modes of the water molecules. 

Peter

Sent from my iPhone

> On May 16, 2017, at 8:53 AM, luca maggi  wrote:
> 
> Hi Peter,
> 
> Thanks  for your answer...but my system is composed by a protein and  a 
> membrane plus the water. The  Calphas are just 438, so I don't think that 
> number is referred to alpha carbons. Moreover I didn't set my calculation in 
> order to calculate the  Calpha eigenvectors...
> 
> 
> 
> 
> Da: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  per conto di Peter Stern 
> 
> Inviato: lunedì 15 maggio 2017 23.14
> A: gmx-us...@gromacs.org
> Oggetto: Re: [gmx-users] NMA eigenvectors doubts
> 
> Perhaps just the eigenvectors for the Calpha atoms.
> 
> Peter
> 
> Sent from my iPhone
> 
> On May 15, 2017, at 9:30 PM, luca maggi 
> mailto:maggi_l...@hotmail.it>> wrote:
> 
> Dear Gromacs Users,
> 
> 
> I have performed a normal mode analysis with gromacs. I have calculated the 
> hessian matrix and the related eigenvalues and eigenvectors. At this point  I 
> needed to extract some elements from the  eigenvectors  and using the dump 
> tool of gromacs I wrote the first of them in a file, but I realised something 
> unexpected. The vector is composed by 7952 row and three columns. My system 
> is composed by about 127000 atoms, thus I expected to find a vector with 
> 127000 x 3 entries...but this number (7952) does not fit at all with my 
> expectation. It seems to be related with the number of steps performed during 
> the normal mode analysis but i cannot understand why
> 
> How has this vector been calculated ?
> 
> 
> Suggestion and hints would be really appreciated!!
> 
> 
> Thanks
> 
> 
> Luca
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Re: [gmx-users] NMA eigenvectors doubts

[Peter Stern]

Perhaps just the eigenvectors for the Calpha atoms.

Peter

Sent from my iPhone

On May 15, 2017, at 9:30 PM, luca maggi 
mailto:maggi_l...@hotmail.it>> wrote:

Dear Gromacs Users,


I have performed a normal mode analysis with gromacs. I have calculated the 
hessian matrix and the related eigenvalues and eigenvectors. At this point  I 
needed to extract some elements from the  eigenvectors  and using the dump tool 
of gromacs I wrote the first of them in a file, but I realised something 
unexpected. The vector is composed by 7952 row and three columns. My system is 
composed by about 127000 atoms, thus I expected to find a vector with 127000 x 
3 entries...but this number (7952) does not fit at all with my expectation. It 
seems to be related with the number of steps performed during the normal mode 
analysis but i cannot understand why

How has this vector been calculated ?


Suggestion and hints would be really appreciated!!


Thanks


Luca
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Re: [gmx-users] Regarding topology creation

[Peter Stern]

Hi,

OT1 and OT2 are only for the C-terminal amino acids and for one glycine it is 
both N-terminal and C-terminal.
For everything else you need to use change it to O.
You will have the same problem with H1, etc.  Except for N-terminal aa it needs 
to be HN.

Regards,
Peter


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Dilip H 
N
Sent: Sunday, April 02, 2017 6:23 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Regarding topology creation

Hello,
I want to create a topology for n glycine molecules
I have 1 glycine molecule and in charmm FF i am able to get the topology of 
1glycine molecule, but now i have few more glycine molesules in .pdb format, 
but if i give the command gmx pdb2gmx -f gly.pdb -o gly.gro it shows the 
following error..
Fatal error:
Atom OT1 in residue GLY 1 was not found in rtp entry GLY with 9 atoms while 
sorting atoms.

But when i gave the same command for 1 glycine molecule to create the topology, 
the topology file was created, but now it is not creating (for more glycine 
molecules).. why is this happening.?? since the same OT1 is also present in 1 
glycine molecule, why is the above error message coming for more molecules..??

here is the 1 molecule glycine.pdb (only residue)

ATOM  1  N   GLY

ATOM  2  H1  GLY

ATOM  3  H2  GLY

ATOM  4  H3  GLY

ATOM  5  CA  GLY

ATOM  6  HA1 GLY

ATOM  7  HA2 GLY

ATOM 8 C GLY

ATOM  9  OT1 GLY

ATOM 10  OT2 GLY

Thank you

--
With Best Regards,

DILIP.H.N
Ph.D Student



   Sent with Mailtrack 

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Re: [gmx-users] QUERY IN GRO FILE

[Peter Stern]

Those are not two different commands, rather the same command with different 
options.
If you are not familiar with the options of the command, then

mdrun -h

will list them for you.  Specifically, in the second instance of mdrun you get 
the default output file name confout.gro whereas in the first instance you have 
changed all the output files to be em.sometype.

Peter 

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Neha 
Gupta
Sent: Thursday, March 30, 2017 8:53 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] QUERY IN GRO FILE

Hi gromacs users,


I have a doubt in this command,

grompp -f em.mdp -c conf.gro -p topol.top -o em


mdrun -v -deffnm em


These commands generate em.gro, em.tpr, em.trr, em.log file.


There is another command which is


mdrun -s em.tpr

which generates confout.gro

Does em.gro and confout.gro are one and the same?

What are the technical differences?


Thanks,

Neha
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Re: [gmx-users] mixed, double precision

[Peter Stern]

I think so.  There is not much meaning to the input/output precision since no 
coordinates are more than single precision.  The purpose of double precision is 
to prevent computational errors arising from accumulated roundoff errors, for 
example, in normal mode analysis where computations involving large matrices 
are required.  But by the same token, such a series of runs may not be 
reproducible.

Regards,
Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Joel 
Markgren
Sent: Monday, February 20, 2017 1:09 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] mixed, double precision

Gooday dear Gromacs users,
I have access to a 5.1.4 version of gromacs compiled in double precision on a 
cluster.

I equilibrated a couple of samples for NVT and NPT and used following commands: 
(the ... means that the rest of the input commands are not relevant for the 
question).

gmx_mpi grompp ... -o nvt.tpr

gmx_mpi_d mdrun -v -deffnm nvt

gmx_mpi grompp ... -c nvt.gro  -o npt.tpr

gmx_mpi_d mdrun -v -deffnm

I realized after the runs that I forgot to specify that I wish to use the 
grompp commands in double precision (gmx_mpi_d grompp).

Have I understood it correctly, that when grompp receives input from a run made 
in double precision, it will produce an output in mixed precision, if not 
specified to do it in double precision? When the mdrun gets the input which is 
in mixed precision it will still make the run in double precision even if the 
input is in mixed.

Have I lost some of the precision between the runs, with risks of energy drifts?

I see it's a bit messy but I hope you understand. Please let me know if you 
need more info or clarifications to answer my question.

Thanks in advance for taking you time to answer my questions.

Regards

Joel Markgren
PhD student in Biology

Sveriges lantbruksuniversitet
Swedish University of Agricultural Sciences

Department of Plant Breeding
PO Box 101, Sweden 23053 Lund
Visiting address: Sundsvägen 10, 23053 Lund
Mobile: +46 706101128
joel.markg...@slu.se, www.slu.se 
[https://internt.slu.se/PageFiles/81117/SLU_Logo_mail.png]

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Re: [gmx-users] Regarding g_energy of heterogenous systems

[Peter Stern]

It is given in well-define units: Kilojoules per mole.  A mole contains an 
Avogadro's number worth of molecules: ~6.022 X 10**23.
What would dividing by the total number of molecules gives you?

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
Apramita Chand
Sent: Tuesday, January 10, 2017 8:53 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Regarding g_energy of heterogenous systems

Dear All,
In the calculation of various energy terms (Coulombic/LJ) for interaction 
energies between Protein-Solvent systems , do we need to specify -nmol as total 
number of molecules of protein and solvent molecules?
If the -nmol option is not specified, the energy value which comes as output as 
, for instance :
LJ-SR -Protein-SOL -   -52.9383 kJ/mol
Should it be divided by total number of molecules(protein+sol) to arrive at the 
value?
Please advise.

yours sincerely,
Apramita Chand
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Re: [gmx-users] Force filed for phosphorylated residues

[Peter Stern]

Hi,

Check the documentation:
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Amir Zeb
Sent: Monday, December 12, 2016 9:35 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Force filed for phosphorylated residues

Hello Mark,

Please help me for this issue

I want to simulate a protein where ser is phosphorylated. i used charm26 ff but 
i m getting this error "Atom P in residue SER 4 was not found in rtp entry SER 
with 11 atoms while sorting atoms". can you please suggest me any possible 
solution for this issue?

Thanks in advance

On Sun, Dec 11, 2016 at 11:22 PM, Mark Abraham 
wrote:

> Hi,
>
> It might be easier to help you with all four of the things I asked you 
> about.
>
> Mark
>
> On Mon, 12 Dec 2016 17:26 Seera Suryanarayana  wrote:
>
> > Dear Mark,
> >
> > I have used the charm36 force field. In c.tdb following atoms are there.
> >
> > ; CHARMM CTER
> >
> > [ COO-  ]
> > [ replace ]
> >  C C  CC12.011  0.34
> >  O OT1  OC15.9994  -0.67
> >  OXT  OT2  OC15.9994  -0.67
> >
> > [ add ]
> >
> >  28OT  C CA N
> >
> >  OC  15.4  -0.67-1
> >
> > [ impropers]
> >
> >  C CA OT2 OT1
> >
> > and in rtp file for GLN  with other atoms they mentioned only one 'O'
> > atom. They didn't give the terminal O atom information.
> >
> > Kindly tell me how to overcome this problem.
> >
> > Thanks in advance
> > Surya
> >
> >
> > Hi,
> >
> > What atoms do you have in that residue, what's in the c.tdb and .rtp 
> > for GLN in force field and what did you choose for termini?
> >
> > Mark
> >
> >  I have one protein with phosphoserine and phosphothreonine. I want 
> > to  do simulation, but I do not know which force field I have to 
> > use. None  of the force field from gromacs has the information of 
> > phospho  residues. Then I tried with charm36, but did work. Kindly 
> > suggest me  what I can do.
> >
> >
> >  Well, CHARMM36 has everything you need included, so unless you 
> > explain  what "didnot work" means (because it's the single most 
> > useless phrase  in debugging  anything), there's little anyone can 
> > do to help you.  Please describe  exactly what the problem was 
> > (commands, output, errors, etc).
> >
> >  -Justin
> >
> >
> >
> >  Dear Justin,
> >
> >  I solved the problem. That is only the mismatching of residue names  
> > and I renamed the residues in my PDB file. Now the problem is with 
> > OXT  atom at C-terminal end.I other words the exact error is "Atom 
> > OXT in  residue GLN 68 was not found in rtp entry GLN with 17 atoms 
> > while  sorting the atoms ". I understood the error. rtp file does 
> > not  have  the atom OXT information. How could one solve this problem?
> >
> > Surya
> > Graduate student
> > India.
> > --
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Re: [gmx-users] GMXSCRIPT: Simple checkpointed Python scripting framework for Gromacs

[Peter Stern]

I guess that Pedro clearly knows that since he refers to it on his page and 
explains why his is different.

Cheers, 
Peter

Sent from my iPad

> On May 6, 2016, at 12:22 PM, João M. Damas  wrote:
> 
> There is already a similar project going on for a long time:
> https://orbeckst.github.io/GromacsWrapper/
> 
> Cheers,
> João
> 
> On Wed, May 4, 2016 at 3:12 AM, Pedro Lacerda 
> wrote:
> 
>> Installation is now working. The upload script was broken.
>> 
>> 2016-05-03 21:50 GMT-03:00 Pedro Lacerda :
>> 
>>> Hi Gromacs users,
>>> 
>>> I just started to develop a scripting framework for Gromacs, it makes
>> some
>>> assumptions about the directory structure and command parameters. You
>>> cannot prepare or run two different systems in the same directory and
>>> always pass the -deffnm option to mdrun.
>>> 
>>> It is very nice!
>>> 
>>> Its main goal is to easy the reproduction of simulation protocols,
>>> canonical steps used to perform and analyze a simulation. The commands
>> are
>>> stored in very readable and structured Python file that requires no
>>> programming knowledge except syntax. Of course you can always extend it
>>> with code as you need.
>>> 
>>> As a bonus it maintain in the .gmx/ directory a checkpoint file that skip
>>> previously successful commands if started again. Also there is no need to
>>> source GMXRC in common cases.
>>> 
>>>https://github.com/pslacerda/gmx
>>> 
>>> Please make comments, suggestions and critics about GMXSCRIPT. The next
>>> feature would be an option to generate a file that allows to reproduce a
>>> simulation in any linux computer with Gromacs installed.
>>> 
>>> (apologies for my poor English!)
>>> 
>>> Best regards,
>>> Pedro Lacerda
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> 
> 
> 
> -- 
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
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Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

[Peter Stern]

As James said, if you are using Discovery Studio it can model missing atoms and 
residues.  But why are you deleting a residue?  What do you hope to learn from 
this?  And don't just ignore missing atoms.

I also don't understand the genion error, but I don't think you reported it 
exactly.  Didn't genion ask you to choose a solvent group and did you do that 
correctly?  I certainly didn't mean that you should choose 1612 sol molecules 
and 11 Na.  I simply meant that I didn't understand the error message since 
17732 is divisible by 11.  I suspect that you didn't choose the correct group 
for solvent.

Since you are a beginner may I suggest that you use one of the many Gromacs 
tutorials available choosing one appropriate to what you are trying to do?  I 
am sure that you can find these easily enough with Google.

Best regards?
Peter

Sent from my iPhone

> On 17 Mar 2016, at 12:27 PM, Pradip Kaur  wrote:
> 
> actually i m not getting how to proceed futher i m beginner to GROMACS
> it would be helpful if you can elaborate the process
> 
>> On 17 March 2016 at 21:54, Pradip Kaur  wrote:
>> 
>> so should i go for sol molecules :1612
>> Na :11
>> 
>>> On 17 March 2016 at 21:44, Peter Stern  wrote:
>>> 
>>> Missing atoms in GLU 474 is because the coordinates for the GLU side
>>> chain weren't resolved in the crystallographic data and aren't included in
>>> the pdb file.  Long bonds are probably because of missing residues.  Check
>>> the pdb file for MISSING residues and atoms (listed in the header
>>> records).  Also, you can't just delete a residue and let Gromacs think that
>>> the preceding and following residues are connected (by an unphysical "long"
>>> bond).  The same goes for missing residues in the pdb file.
>>> 
>>> I hope that the net charge was -5.999 otherwise, why add Na ions.  And as
>>> far as I know, 11*1612=17732.
>>> 
>>> Peter Stern
>>> 
>>> Sent from my iPad
>>> 
>>> On 17 במרץ 2016, at 11:08, Pradip Kaur >> kaur.pradip...@gmail.com>> wrote:
>>> 
>>> i am currently working with 2bbo.pdb protein ,i have edited this protein
>>> in
>>> Discovery studio 4.5 and deleted phenylalanine at 508 position , now i m
>>> running molecular dynamics simulation  in GROMACS 5.0.2 bt after running
>>> pdb2gmx  with  GROMOS96 53a6 force field Water model :spc216 ,it is
>>> showing
>>> 
>>> Warning: Long Bond (161-163 = 1.78456 nm)
>>> 
>>> Warning: Long Bond (840-842 = 0.357037 nm)
>>> 
>>> Warning: Long Bond (2237-2239 = 0.636287 nm)
>>> 
>>> 
>>> 
>>> WARNING: atom CG is missing in residue GLU 474 in the pdb file
>>> 
>>> 
>>> 
>>> 
>>> 
>>> WARNING: atom CD is missing in residue GLU 474 in the pdb file
>>> 
>>> 
>>> 
>>> 
>>> 
>>> WARNING: atom OE1 is missing in residue GLU 474 in the pdb file
>>> 
>>> 
>>> 
>>> 
>>> 
>>> WARNING: atom OE2 is missing in residue GLU 474 in the pdb file
>>> 
>>> 
>>> 
>>> 
>>> 
>>> ---
>>> 
>>> Program pdb2gmx, VERSION 5.0.2
>>> 
>>> Source code file:
>>> /build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/pdb2top.cpp, line:
>>> 1587
>>> 
>>> 
>>> 
>>> Fatal error:
>>> 
>>> There were 4 missing atoms in molecule Protein_chain_A, if you want to use
>>> this incomplete topology anyhow, use the option -missing
>>> 
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> 
>>> website at http://www.gromacs.org/Documentation/Errors
>>> 
>>> 
>>> *But  after ignoring missing atoms ,when i am running grompp command it
>>> shows that the system has non zero integral charge of 5.999.*
>>> 
>>> *i have added command genion to neutalise the charge by adding 6 Na ions
>>> .After running the command it says that you have generated 17732 solvent
>>> molecules which are not multiple of 11 .*
>>> 
>>> *can any one help me with this problem*
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>> 
>>> *

Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

[Peter Stern]

Missing atoms in GLU 474 is because the coordinates for the GLU side chain 
weren't resolved in the crystallographic data and aren't included in the pdb 
file.  Long bonds are probably because of missing residues.  Check the pdb file 
for MISSING residues and atoms (listed in the header records).  Also, you can't 
just delete a residue and let Gromacs think that the preceding and following 
residues are connected (by an unphysical "long" bond).  The same goes for 
missing residues in the pdb file.

I hope that the net charge was -5.999 otherwise, why add Na ions.  And as far 
as I know, 11*1612=17732.

Peter Stern

Sent from my iPad

On 17 במרץ 2016, at 11:08, Pradip Kaur 
mailto:kaur.pradip...@gmail.com>> wrote:

i am currently working with 2bbo.pdb protein ,i have edited this protein in
Discovery studio 4.5 and deleted phenylalanine at 508 position , now i m
running molecular dynamics simulation  in GROMACS 5.0.2 bt after running
pdb2gmx  with  GROMOS96 53a6 force field Water model :spc216 ,it is showing

Warning: Long Bond (161-163 = 1.78456 nm)

Warning: Long Bond (840-842 = 0.357037 nm)

Warning: Long Bond (2237-2239 = 0.636287 nm)



WARNING: atom CG is missing in residue GLU 474 in the pdb file





WARNING: atom CD is missing in residue GLU 474 in the pdb file





WARNING: atom OE1 is missing in residue GLU 474 in the pdb file





WARNING: atom OE2 is missing in residue GLU 474 in the pdb file





---

Program pdb2gmx, VERSION 5.0.2

Source code file:
/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/pdb2top.cpp, line:
1587



Fatal error:

There were 4 missing atoms in molecule Protein_chain_A, if you want to use
this incomplete topology anyhow, use the option -missing

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors


*But  after ignoring missing atoms ,when i am running grompp command it
shows that the system has non zero integral charge of 5.999.*

*i have added command genion to neutalise the charge by adding 6 Na ions
.After running the command it says that you have generated 17732 solvent
molecules which are not multiple of 11 .*

*can any one help me with this problem*
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Re: [gmx-users] Minimising forces for vibrational normal mode analysis

[Peter Stern]

This is a non-problem.  You will never get zero eigenvalues for such a large 
system since you are not at an absolute minimum.  The fact that you got no 
negative eigenvalues and the six lowest eigenvalues are very small (surely 
much, much smaller than the subsequent eigenvalues) indicates that you are at a 
reasonably good minimum. But don't be misled. Another (different) minimization 
could bring the system to a different minimum (also good) with somewhat 
different eigenvalues and eigenvectors.

Regards,
Peter Stern

Sent from my iPhone

> On 29 Feb 2016, at 3:23 PM, Nash, Anthony  wrote:
> 
> Hi all,
> 
> Hoping this will be the final stumbling block. I’ve successfully minimised
> my structure to a a very small max force:
> Potential Energy  = -1.93736854460113e+03
> Maximum force =  7.39399083846082e-04 on atom 34
> Norm of force =  1.64068483698544e-04
> 
> 
> When I perform integrator=nm there are no warning of potential imaginary
> (negative) values. However, upon running:
> g_nmeig_d -f dogdic_nma.mtx -s dogdic_nma.tpr -last 3000
> I see the following:
> 
> 
> 
> Full matrix storage format, nrow=279, ncols=279
> Diagonalizing to find vectors 1 through 279...
> 
> One of the lowest 6 eigenvalues has a non-zero value.
> 
> This could mean that the reference structure was not
> properly energy minimized.
> Writing eigenvalues...
> 
> Back Off! I just backed up eigenval.xvg to ./#eigenval.xvg.2#
> Writing eigenfrequencies - negative eigenvalues will be set to zero.
> 
> 
> 
> 
> My lowest 6 eigenvalues are:
> 1   0.0780823
> 20.153357
> 30.174772
> 40.327362
> 50.466203
> 6 0.64693
> 
> 
> I’m a little confused by the statement "One of the lowest 6 eigenvalues
> has a non-zero value. This could mean that the reference structure was not
> properly energy minimized.” Really? Surely it out to be if one or more of
> the values is negative.  Also, there were no eigenvalues set to zero
> (hence, I can only assume I have no negative eigenvalues).
> 
> Would appreciate a little insight.
> Many thanks
> Anthony
> 
> Dr Anthony Nash
> Department of Chemistry
> University College London
> 
> 
> 
> 
> 
> On 29/02/2016 16:25, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
> behalf of Nash, Anthony"
>  a.n...@ucl.ac.uk> wrote:
> 
>> Dear Mark and Justin,
>> 
>> By removing the restraints (your suggestions) it appears to have worked!
>> 
>> Maximum force: 9.21098e-04
>> Writing Hessian...
>> 
>> This now matches the same force as my energy minimisation. Many thanks for
>> you help.
>> 
>> Thanks
>> Anthony
>> 
>> 
>> 
>> Dr Anthony Nash
>> Department of Chemistry
>> University College London
>> 
>> 
>> 
>> 
>> 
>> On 29/02/2016 14:46, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
>> behalf of Mark Abraham" > on behalf of mark.j.abra...@gmail.com> wrote:
>> 
>>> Hi,
>>> 
>>> An earlier mdp file suggested you were using position restraints. There
>>> should be no need for this, nor any problem, but what happens without
>>> them?
>>> 
>>> Mark
>>> 
>>>> On Mon, 29 Feb 2016 15:39 Nash, Anthony  wrote:
>>>> 
>>>> Hi Justin,
>>>> 
>>>> After some digging I had found that link and made some adjustments (as
>>>> presented in the later email).
>>>> 
>>>> After a series of energy minimisations (including switching LINCS off,
>>>> and
>>>> dropping the energy step to a very small number), and with the final
>>>> command:
>>>> grompp_d -f cg.mdp -c modic_cg_3.gro -p system.top -o modic_cg_4 -t
>>>> modic_cg_3.trr
>>>> 
>>>> 
>>>> Polak-Ribiere Conjugate Gradients converged to Fmax < 0.001 in 6883
>>>> steps
>>>> Potential Energy  = -1.92681826422996e+03
>>>> Maximum force =  8.54361662283108e-04 on atom 44
>>>> Norm of force =  2.71110116926712e-04
>>>> 
>>>> 
>>>> However, when switching to integrator=nm, running grompp_d -f nma.mdp
>>>> -c
>>>> modic_cg_4.gro -p system.top -o modic_nma -t modic_cg_4.trr, and then
>>>> mdrun_d, I get:
>>>> 
>>>> Maximum force: 5.19179e+01
>>>> The force is probably not small enough to ensure that you are at a
>>>

Re: [gmx-users] trjconv - two chains are separated

[Peter Stern]

I have also encountered this problem and was able to solve it using the tpr 
file generated before running editconf as the input to trjconv (with -pbc no 
jump).

Peter

Sent from my iPad

> On 3 בפבר׳ 2016, at 4:51, Catarina A. Carvalheda dos Santos 
>  wrote:
> 
> Hi there,
> 
> I had similar problems in the past. You'll have to play with trjconv and
> find the best combination of different flags to solve the visualization
> problem.
> 
> You can start by trying out this workflow for example:
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> 
> Hope this helps.
> 
> Good luck!
> 
> 
> 
> On 3 February 2016 at 06:15, Trayder Thomas 
> wrote:
> 
>> For "-pbc nojump" to work, you need to make sure they are together (as you
>> want) in the first frame of your input trajectory.
>> 
>> The most reliable way to do this is by centering the trajectory on a
>> residue at the interface between the two chains (using a custom index
>> group).
>> 
>> I've also heard some people have had luck with "-pbc cluster"
>> 
>> You can then run "-pbc nojump" on the centered (or clustered) trajectory.
>> 
>> -Trayder
>> 
>> 
>> 
>> 
>>> On Wed, Feb 3, 2016 at 9:37 AM, Yunlong Liu  wrote:
>>> 
>>> Hi Gromacs Users,
>>> 
>>> I used "gmx trjconv" (Gromacs 5.0.4) to remove the pbc of my
>> trajectories.
>>> My protein has two chains (A and B) and they closely bind to each other.
>>> after running trjconv with "-pbc nojump", two chains are greatly
>> separated
>>> by a certain distance. It is mostly likely that the pbc is not
>> successfully
>>> removed and the program takes a chain from one unit cell and another from
>>> another unit cell.
>>> 
>>> Does anybody have any idea to solve the problem?
>>> 
>>> Best
>>> Yunlong
>>> --
>>> Gromacs Users mailing list
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>>> send a mail to gmx-users-requ...@gromacs.org.
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>> Gromacs Users mailing list
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>> posting!
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>> send a mail to gmx-users-requ...@gromacs.org.
>> 
>> The University of Dundee is a registered Scottish Charity, No: SC015096
> 
> 
> 
> -- 
> Catarina A. Carvalheda
> 
> PhD Student
> Computational Biology Division
> SLS & SSE
> University of Dundee
> DD1 5EH, Dundee, Scotland, UK
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Re: [gmx-users] disabling pbc while using trjconv

[Peter Stern]

First try the trjconv option -pbc no jump.

Peter

Sent from my iPad

> On 20 בינו׳ 2016, at 19:50, Irem Altan  wrote:
> 
> Hi,
> 
> When generating trajectories with trjconv in .pdb format, is it possible to 
> have the coordinates unwrapped? What I mean by this is to have coordinates 
> the way they were in the original protein .pdb file: not wrapped into the 
> unit cell (so that the protein is a single piece).
> 
> Best,
> Irem
> -- 
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Re: [gmx-users] Gromacs Tutorial

[Peter Stern]

The only thing that you can do about this is to learn from the experience and 
in the future, copyright everything that you create and distribute.  Then 
nobody can "plagiarize" your work without your permission.

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Tuesday, January 19, 2016 3:01 PM
To: mdgroup; Discussion list for GROMACS users
Subject: [gmx-users] Gromacs Tutorial

Hey :)

As some of you know, some years ago I developed an extensive Gromacs tutorial 
(at the University of Utrecht). That work has caught they eye of educators, and 
now the tutorial is published as an educational paper! Just kind of funny that 
I'm not an author.
For those interested:

http://onlinelibrary.wiley.com/doi/10.1002/bmb.20941/abstract

Enjoy!

Tsjerk

--
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Re: [gmx-users] Installation of two versions of Gromacs on one system

[Peter Stern]

Hi Tushar,

I think that you are confused.  I was answering Indu's question, not asking it.

Regards,
Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tushar 
Ranjan Moharana
Sent: Thursday, January 14, 2016 2:13 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Installation of two versions of Gromacs on one system

Hi Peter,
Try this whenever opening a new terminal source /path/to/gromacs/bin/GMXRC

What ever version you want to use mention corresponding path.


"A society with free knowledge is better than a society with free food"

Best Regards

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB, INDIA
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Re: [gmx-users] Help for gmx enemat

[Peter Stern]

Hi Valerio,

Sorry, I don't know then.

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of valerio 
di giulio
Sent: Wednesday, January 13, 2016 11:17 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Help for gmx enemat

Hi Peter,

I have already created  an index file with make_ndx in which I specify what 
atoms are in DNA1 and DNA2 groups. Moreover the two groups are present in the 
file topol.top. Indeed GROMACS doesn't produce any error about the declaration 
of them in the file .mdp. I send you also my topol.top file for clarity:
.

; GROMACS topology
;
; Include the force field
#include "/amber03.ff/forcefield.itp"

; Include chain topologies
#include "topol1.itp"
#include "topol2.itp"

; Include water topology
#include "amber03.ff/tip4p.itp"

; Include generic ion topology
#include "amber03.ff/ions.itp"

[ system ]
Two all-AT in water

[ molecules ]
DNA11
DNA21
SOL 39390
NA   190
CL   146

.....

Thanks,

Valerio

2016-01-13 20:40 GMT+01:00 Peter Stern :

> I believe that you need to define which nucleotides are in each group 
> DNA1 and DNA2 using make_ndx, since those are not "default" groups.  I 
> think that you can do this and then do an Metin -rerun just to define 
> the new groups.
>
> Peter
>
> Sent from my iPad
>
> > On 13 בינו׳ 2016, at 20:53, valerio di giulio 
> > 
> wrote:
> >
> > Hi,
> >
> > I have a problem with the use of "gmx enemat". I'm trying to 
> > calculate the contribution of SH-LJ to the potential that exists 
> > between two DNA strands with GROMACS 5.1.1. I've already got a 
> > Potential of Mean Force doing an umbrella sampling.
> > For this reason I have already many files .edr each one linked to a
> window,
> > from
> > which I would like to extract the SH-LJ contribution but every time 
> > I use "enemat" this is the output:
> >
> > ..
> >
> > GROMACS:  gmx enemat, VERSION 5.1.1
> > Executable:   /usr/local/gromacs/bin/gmx
> > Data prefix:  /usr/local/gromacs
> > Command line:
> >  gmx enemat umbrella1e.edr -ljsr
> >
> > Opened ener.edr as single precision energy file Will read groupnames 
> > from inputfile Read 2 groups group 0WARNING! could not find group 
> > Coul-SR:DNA1-DNA1 (0,0)in energy
> file
> > WARNING! could not find group LJ-SR:DNA1-DNA1 (0,0)in energy file 
> > WARNING! could not find group Coul-SR:DNA1-DNA2 (0,1)in energy file 
> > WARNING! could not find group LJ-SR:DNA1-DNA2 (0,1)in energy file 
> > group 1WARNING! could not find group Coul-SR:DNA2-DNA2 (1,1)in 
> > energy
> file
> > WARNING! could not find group LJ-SR:DNA2-DNA2 (1,1)in energy file
> >
> > Will select half-matrix of energies with 0 elements Last energy 
> > frame read 500 time  500.000 Will build energy half-matrix of 2 
> > groups, 0 elements, over 501 frames Segmentation fault (core dumped)
> >
> > ...
> >
> > Although I have written to the .mdp file:
> >
> > energygrps = DNA1 DNA2
> >
> > Thank you in advance,
> >
> > Valerio Di Giulio
> > --
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Re: [gmx-users] Installation of two versions of Gromacs on one system

[Peter Stern]

Are you sure that the command g_rms_mod appears in your gromacs bin directory, 
because I don't see it in mine?
And did you source the GMXRC file in your gromacs bin directory?

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Indu 
Kumari
Sent: Wednesday, January 13, 2016 9:56 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Installation of two versions of Gromacs on one system

Good afternoon sir/ma'am,

I am using Gromacs-4.6.5 on my system (Ubuntu14.04LTS). I want to install
Gromacs-4.5.6 on the same system. I have tried to install it as tutorial 
available on Gromcas site, but after sudo make install command, when I tried to 
run commands:
g_rms_mod

It give error: command not found.

All the commands are there in the "build" directory, but they are not 
recognised.

Please help.


With regards,
*Indu Kumari*
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Re: [gmx-users] Help for gmx enemat

[Peter Stern]

I believe that you need to define which nucleotides are in each group DNA1 and 
DNA2 using make_ndx, since those are not "default" groups.  I think that you 
can do this and then do an Metin -rerun just to define the new groups.

Peter

Sent from my iPad

> On 13 בינו׳ 2016, at 20:53, valerio di giulio  
> wrote:
> 
> Hi,
> 
> I have a problem with the use of "gmx enemat". I'm trying to calculate
> the contribution of SH-LJ to the potential that exists between two DNA
> strands with GROMACS 5.1.1. I've already got a Potential of Mean Force
> doing an umbrella sampling.
> For this reason I have already many files .edr each one linked to a window,
> from
> which I would like to extract the SH-LJ contribution but every time I use
> "enemat" this is the output:
> 
> ..
> 
> GROMACS:  gmx enemat, VERSION 5.1.1
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Command line:
>  gmx enemat umbrella1e.edr -ljsr
> 
> Opened ener.edr as single precision energy file
> Will read groupnames from inputfile
> Read 2 groups
> group 0WARNING! could not find group Coul-SR:DNA1-DNA1 (0,0)in energy file
> WARNING! could not find group LJ-SR:DNA1-DNA1 (0,0)in energy file
> WARNING! could not find group Coul-SR:DNA1-DNA2 (0,1)in energy file
> WARNING! could not find group LJ-SR:DNA1-DNA2 (0,1)in energy file
> group 1WARNING! could not find group Coul-SR:DNA2-DNA2 (1,1)in energy file
> WARNING! could not find group LJ-SR:DNA2-DNA2 (1,1)in energy file
> 
> Will select half-matrix of energies with 0 elements
> Last energy frame read 500 time  500.000
> Will build energy half-matrix of 2 groups, 0 elements, over 501 frames
> Segmentation fault (core dumped)
> 
> ...
> 
> Although I have written to the .mdp file:
> 
> energygrps = DNA1 DNA2
> 
> Thank you in advance,
> 
> Valerio Di Giulio
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Re: [gmx-users] Serine phosphorylation

[Peter Stern]

The instructions for adding a new residue are here:
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=add+new+residue

If you cannot understand these instructions, then most probably you will have 
to read about them in Chapter 5 of the gromacs manual in order to understand 
what all the different files mentioned are about.  In particular, you will have 
to define a new residue, e.g. SERP or something like that  in  the 
residuetypes.dat file, but also in the aminoacids.rtp file making sure that all 
the new bonds, angles and dihedrals are defined and that these also exist in 
the ffbonded.itp file.  The biggest challenge will be assigning the correct 
charges to the atoms of the new residue so that the net charge is now, for 
example,  -1.  One way to do this is to run Gaussian.  You need to google this 
a bit.

Regards,
Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Simone 
Bolognini
Sent: Sunday, January 10, 2016 11:08 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Serine phosphorylation

Thank you for your support, but I find the instructions on the website 
extremely unclear to me. There are some commands to be run which are nor 
gromacs neither bash commands that pretty puzzle me. However, I'd better be 
more specific in explaining my problem: I have a protein whose pdb contains a 
particular serine in which I am interested on. Now, for some reasons, I need to 
change this serine (and only this one!) to a phosphorylated one and run some MD 
production using AMBER-ILDN with this new configuration. What should I do 
exactly? Can you provide me a sequence of steps which I should follow in order 
to go from the starting pdb to the actual simulation?

As always, thank you very much for your help!
Simone

Il giorno ven 8 gen 2016 alle ore 13:30 Changrong Ge  
ha scritto:

> http://selene.princeton.edu/FFPTM/
>
> On Fri, Jan 8, 2016 at 9:52 AM, Simone Bolognini 
>  >
> wrote:
>
> > Hi everyone,
> > I need to run some MD simulations with a protein where a particular
> serine
> > should be phosphorylated. Since in the original pdb the serine is
> actually
> > not, I guess I should modify something 'by hand'. I'm going to use 
> > AMBER-ILDN ff. Can anyone of you tell me what should I do? My first 
> > guess was to generate the topology and then directly substitute my 
> > serine with the phosphorylated one (looking for the AMBER-ILDN 
> > parameters), but sincerely I don't know if this is the correct way to 
> > proceed.
> >
> > Thanks a lot for your support!
> > Simone
> > --
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
> > posting!
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> > or send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
>
> Changrong Ge, PhD
>
> Division of Medical Inflammation Research Department of Medical 
> Biochemistry and Biophysics (MBB) Karolinska Institutet Scheeles väg 
> 2, B2 Plan 4
> SE-171 77 Stockholm
> Sweden
> Tel:  +46-8-524 86337 ,   Mobile: +46-(0)76-2878 029
> Fax: +46-8-524 87750 ,  Email: changrong...@ki.se 
>  or changrong...@gmail.com
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Re: [gmx-users] Generating topology of 3b68.ent

[Peter Stern]

Look for any "MISSING ATOMS" in the pdb file (in the REMARKS).
Look at the coordinates given for the LYS in question and check if there are 
coordinates for the CG.

Experimental data isn't "perfect."  PDB entries have missing residues and 
missing atoms all the time because they couldn't be resolved.

"Detective work" is over-glamorizing it.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Simone 
Bolognini
Sent: Thursday, January 07, 2016 8:37 PM
To: gmx-us...@gromacs.org
Cc: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Generating topology of 3b68.ent

Hi Mark,
Thank you for your fast aswer. However, I don't quite get what you mean by 
"detective work". What should I exactly look for?
Il 07/gen/2016 19:25, "Mark Abraham"  ha scritto:

> Hi,
>
> It could just be missing from the experimental data. You'll need to do 
> some detective work about that pdb entry.
>
> Mark
>
> On Thu, 7 Jan 2016 19:05 Simone Bolognini 
> wrote:
>
> > Good evening everyone,
> > I was trying to generate the topology of the ligand binding domain 
> > of the human androgen receptor (3B68) with pdb2gmx using pdb2gmx -f 
> > 3b68.ent -o ar.gro -p ar.top -ignh using the AMBER-ILDN ff and 
> > implict solvent (therefore typing 6 and 6
> again
> > on gromacs v. 4.6.5) and it throws me the following error:
> >
> > Fatal error:
> > Residue 177 named LYS of a molecule in the input file was mapped to 
> > an entry in the topology database, but the atom CG used in that 
> > entry is not found in the input file. Perhaps your atom and/or 
> > residue naming needs to be fixed.
> >
> > What am I doing wrong? You can find the .ent here:
> > http://www.rcsb.org/pdb/explore/explore.do?structureId=3b68
> > Thank you very much for your support!!
> >
> > Simone
> > --
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> > posting!
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Re: [gmx-users] bash: genrestr: command not found

[Peter Stern]

This is a unix/linux problem, not a gromacs problem.
And as such, I strongly suggest that you not run such commands as root, but 
rather as an ordinary user.
Running commands as root, especially if you know little or no unix/linux can be 
very dangerous.
The problem is probably in your path.  The shell needs to know where the gmx 
executable is located.
There are several linux approaches to that, but for now, find out where gmx is 
installed, and do the following:
export GMXDIR="location of gmx executable"
source $GMXDIR/GMXRC 

Then it should work.

Regards,
Peter Stern

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Puneet
Sent: Thursday, December 10, 2015 11:17 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] bash: genrestr: command not found

Hello 

 


I am using command 


"genrestr -f jz4.gro -o posre_jz4.itp -fc 1000 1000 1000" for Restraining the 
Ligand but I am facing following error


[root@localhost AD]# gmx genrestr -f lig.gro -o lig.itp -fc 1000 1000 1000

bash: gmx: command not found

[root@localhost AD]#  genrestr -f lig.gro -o lig.itp -fc 1000 1000 1000

bash: genrestr: command not found

 

Kindly tell me where is the problem. Please reply me as soon as possible.

 

Thanks in advance

Puneet

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Re: [gmx-users] atom numbering

[Peter Stern]

Justin already answered your question five days ago:
Use the -norenum option for pdb2gmx

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Marta 
Wisniewska
Sent: Sunday, December 06, 2015 2:03 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] atom numbering

Dear Gromacs users,

My problem focus on number order. I am preparing my system to md. In my pdb 
file I made a some modifications (delete chains or ligand compounds).
During preparation of topology and gro file, the residue number ordering is 
changed. Is there any possibility to preserve number ordering from pdb file 
during pdb2gmx transfer?

Thank you in advance,
Marta
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Re: [gmx-users] Methanol geometry parameters

[Peter Stern]

And there are no bond angles in methanol aside from the ones involving hydrogen 
atoms and these are added automatically by pdb2gmx.
As I already wrote, and Justin pointed out, the only geometric information that 
you need is the C-O bond length, which is given in the force field Ito file.  
For water there are no coordinates, just the single O atom.  Again, H's are 
added.

Sent from my iPhone

> On 4 Dec 2015, at 2:39 PM, Daniele Veclani  wrote:
> 
> Dear Stern.
> 
> I apologize for the disruption.
> 
> Create pdb file is very simple. but the distances and bond angles of
> methanol where I find them?
> 
> I do not think can I put random distances and angles?
> 
> Best
> D.V.
> 
> 
> 
> 2015-12-04 12:50 GMT+01:00 Barnett, James W :
> 
>>> On Fri, 2015-12-04 at 09:43 +0100, Daniele Veclani wrote:
>>> Dear Peter Stern.
>>> 
>>> Yes, I need the starting coordination for methanol, but are there
>> specific
>>> coordinates like for spce water or tip3p water?
>>> 
>>> Where can I find the files .gro or .pdb for methanol ?
>> 
>> Creating a methanol pdb file should be quick with a program like Avogadro
>> or
>> maybe AmberTool's xleap. Then use "gmx solvate" to get coordinates for
>> water.
>> 
>>> 
>>> 
>>> Dear Chaban
>>> 
>>> Similar molecules have already been studied with this methanol.
>>> 
>>> This Methanol is implemented in opls force field.
>>> 
>>> I appreciate the time and effort you have spent sorting out that problem.
>>> 
>>> D.V.
>>> 
>>> 
>>> 2015-12-04 8:41 GMT+01:00 Kalev Takkis :
>>> 
>>>> On 3 December 2015 at 20:05, Vitaly V. Chaban 
>> wrote:
>>>> 
>>>>> You, perhaps, need to care about *compatibility* of this old
>> methanol and
>>>>> your solute molecule.
>>>> 
>>>> 
>>>> Why? General caution or do you know that there is something wrong with
>> it?
>>>> Because if I'm not mistaken, it's the same methanol distributed with
>>>> Gromacs.
>>>> 
>>>> All the best,
>>>> Kalev
>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> On Thu, Dec 3, 2015 at 2:08 PM, Peter Stern <
>> peter.st...@weizmann.ac.il>
>>>>> wrote:
>>>>> 
>>>>>> The force field parameters are defined in ffbonded.itp and
>>>>> ffnonbonded.itp.
>>>>>> You still need starting coordinates for your molecule.
>>>>>> There are plenty of programs which will do this, but you can
>> probably
>>>>> find
>>>>>> it in some pdb entry.
>>>>>> But, it is also trivial to do by hand since there are only two
>> atoms
>>>> and
>>>>>> you know the C-O bond distance, e.g.:
>>>>>> HETATM1  C   MOH  1  1   0.000   0.000   1.410  1.00  1.00
>>>>>> HETATM2  O  MOH  1  1   0.000   0.000   0.000  1.00  1.00
>>>>>> 
>>>>>> You should use an existing pdb or gro file as a template for the
>>>> correct
>>>>>> format.  gmx pdb2gmx will add the H-atoms.
>>>>>> 
>>>>>> Peter Stern
>>>>>> 
>>>>>> -Original Message-
>>>>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
>>>>>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
>>>> Daniele
>>>>>> Veclani
>>>>>> Sent: Thursday, December 03, 2015 3:31 PM
>>>>>> To: gmx-us...@gromacs.org
>>>>>> Subject: Re: [gmx-users] Methanol geometry parameters
>>>>>> 
>>>>>> Thank you for your reply.
>>>>>> 
>>>>>> Yes, The .itp file for methanol comes from gromacs. But but I need
>> the
>>>>>> .gro file. I need the geometric parameters like distances, angles
>> and
>>>>>> diedrals.
>>>>>> these parameters are not in the .itp file or I'm wrong??
>>>>>> 
>>>>>> Best regards
>>>>>> D.V.
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>> 
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_L

Re: [gmx-users] Methanol geometry parameters

[Peter Stern]

The force field parameters are defined in ffbonded.itp and ffnonbonded.itp.
You still need starting coordinates for your molecule.
There are plenty of programs which will do this, but you can probably find it 
in some pdb entry.
But, it is also trivial to do by hand since there are only two atoms and you 
know the C-O bond distance, e.g.:
HETATM1  C   MOH  1  1   0.000   0.000   1.410  1.00  1.00  
HETATM2  O  MOH  1  1   0.000   0.000   0.000  1.00  1.00   

You should use an existing pdb or gro file as a template for the correct 
format.  gmx pdb2gmx will add the H-atoms.

Peter Stern

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Daniele 
Veclani
Sent: Thursday, December 03, 2015 3:31 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Methanol geometry parameters

Thank you for your reply.

Yes, The .itp file for methanol comes from gromacs. But but I need the .gro 
file. I need the geometric parameters like distances, angles and diedrals.
these parameters are not in the .itp file or I'm wrong??

Best regards
D.V.
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Re: [gmx-users] pdb2gmx (ver 5.0.7) - choosing -ter "None" does not work

[Peter Stern]

I have had this problem and I suspect that the answer lies in the Fatal error 
you receive.  Grimace will not allow you to have dangling bonds.  Something has 
to be attached to the first and last bond, otherwise it is not a viable 
molecule.

Peter

Sent from my iPad

> On 2 בדצמ׳ 2015, at 18:03, Yoav Atsmon-Raz  wrote:
> 
> Hi, I've been trying to make an  peptide with removed amine and Carboxyl 
> terminal groups by applying the -ter "none" option of pdb2gmx.
> However, everytime I apply it, it fails in constructing the gro file. If I 
> don't use the -ter option it suceeds making the gro file but makes those 
> groups itself but I'm looking for a way to avoid that. Thanks in advance for 
> anyone answering this. I'm suspecting that its having problems with applying 
> the "none" option from the .c.tdb and .n.tdb options correctly but i'm not 
> sure how to correct this.
> 
> Following is my output:
> 
> -
> GROMACS:  gmx pdb2gmx, VERSION 5.0.7
> Executable:   /usr/local/gromacs/bin/gmx
> Library dir:  /usr/local/gromacs/share/gromacs/top
> Command line:
>  pdb2gmx -f test.pdb -o test -p test.top -ter
> 
> 
> Select the Force Field:
> From '/home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top/':
> 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
> 1999-2012, 2003)
> 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
> 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
> 461-469, 1996)
> 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
> 1049-1074, 2000)
> 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
> 2006)
> 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
> 78, 1950-58, 2010)
> 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
> 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
> 9: GROMOS96 43a1 force field
> 10: GROMOS96 43a2 force field (improved alkane dihedrals)
> 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> 14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
> 10.1007/s00249-011-0700-9)
> 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 8
> 
> Using the Charmm27 force field in directory 
> /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff
> 
> Opening force field file 
> /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/watermodels.dat
> 
> Select the Water Model:
> 1: TIP3P   TIP 3-point, recommended
> 2: TIP4P   TIP 4-point
> 3: TIPS3P  CHARMM TIP 3-point with LJ on H's (note: twice as slow in GROMACS)
> 4: TIP5P   TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
> 5: SPC simple point charge
> 6: SPC/E   extended simple point charge
> 7: None
> 6
> Opening force field file 
> /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/aminoacids.r2b
> Opening force field file 
> /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/rna.r2b
> Reading test.pdb...
> Read 40 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 1 chains and 0 blocks of water and 4 residues with 40 atoms
> 
>  chain  #res #atoms
>  1 'A' 4 40
> 
> All occupancies are one
> Opening force field file 
> /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/atomtypes.atp
> Atomtype 213
> Reading residue database... (charmm27)
> Opening force field file 
> /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/aminoacids.rtp
> Residue 44
> Sorting it all out...
> Opening force field file 
> /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/dna.rtp
> Residue 48
> Sorting it all out...
> Opening force field file 
> /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/lipids.rtp
> Residue 60
> Sorting it all out...
> Opening force field file 
> /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/rna.rtp
> Residue 64
> Sorting it all out...
> Opening force field file 
> /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/aminoacids.hdb
> Opening force field file 
> /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/dna.hdb
> Opening force field file 
> /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/lipids.hdb
> Opening force field file 
> /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/rna.hdb
> Opening force field file 
> /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/aminoacids.n.tdb
> Opening force field file 
> /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/dna.n.tdb
> Opening force field file 
> /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//charmm27.ff/rna.n.tdb
> Opening force field file 
> /home/yoav/Programs/Gromacs/gromacs-5.0.7/share/top//cha

Re: [gmx-users] how to make .trr file readable

[Peter Stern]

http://manual.gromacs.org/online/trr.html

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of bipin 
singh
Sent: Tuesday, December 01, 2015 2:48 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] how to make .trr file readable

http://pythonhosted.org/MDAnalysis/documentation_pages/coordinates/TRR.html


--
Thanks and Regards,
Bipin Singh

On Tue, Dec 1, 2015 at 6:10 PM, Ayesha Kanwal 
wrote:

> Dear Gromacs experts,
> i am very new to Gromacs i only want to take .trr file and make it 
> readable . as i want to use .trr file in my own tool as an input format.
> how can i make it readable and can use it in my tool ?
> Best regards
> Ayesha
>
> --
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Re: [gmx-users] combine two pdb files

[Peter Stern]

Probably.  So follow Chandan Choudhury's suggestion to use editconf -resnr 1 to 
reorder the residue numbers too and then it should work.

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of masoud 
keramati
Sent: Saturday, November 28, 2015 1:12 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] combine two pdb files

hi

yes that's right. but it's renuber atoms not residues.
is the same residue number make an error?

tnx : )

On Sat, Nov 28, 2015 at 1:57 AM, Peter Stern 
wrote:

> AFAIK pdb2gmx doesn't care about the atom numbers in your pdb file 
> since in any case it reorders them and renumbers them after adding 
> hydrogen atoms.  Did you try it?
>
> Regards,
> Peter
>
> Sent from my iPad
>
> > On 27 בנוב׳ 2015, at 22:28, masoud keramati 
> > 
> wrote:
> >
> > Hello
> >
> > I want to simulate two proteins and need to combine these two pdb 
> > files
> in
> > one.
> > important thing is the atom number. if combine with cat command it 
> > gives
> a
> > file that contain two atom with the same atom and residue number 
> > that
> will
> > make an error in simulation.
> > is there exist any way to combine these two pdb files to solve this
> problem?
> > I mean if first pdb finish with atom number n and residue number m 
> > then next pdb is start with atom number n+1 and residue number m+1.
> >
> > tnx
> > --
> > Gromacs Users mailing list
> >
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> > or
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Re: [gmx-users] combine two pdb files

[Peter Stern]

AFAIK pdb2gmx doesn't care about the atom numbers in your pdb file since in any 
case it reorders them and renumbers them after adding hydrogen atoms.  Did you 
try it?

Regards,
Peter

Sent from my iPad

> On 27 בנוב׳ 2015, at 22:28, masoud keramati  wrote:
> 
> Hello
> 
> I want to simulate two proteins and need to combine these two pdb files in
> one.
> important thing is the atom number. if combine with cat command it gives a
> file that contain two atom with the same atom and residue number that will
> make an error in simulation.
> is there exist any way to combine these two pdb files to solve this problem?
> I mean if first pdb finish with atom number n and residue number m then
> next pdb is start with atom number n+1 and residue number m+1.
> 
> tnx
> -- 
> 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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Re: [gmx-users] service broken?

[Peter Stern]

Hi,

I just tried and had no problem, so maybe it's some setting on your end?
Otherwise, it would be more appropriate to contact the MacKerell group about 
this and not the gromacs list:
a...@outerbanks.umaryland.edu

Regards,
Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Albert
Sent: Thursday, November 26, 2015 9:00 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] service broken?

Hello:

I am trying to download the latest CHARMM forcefield for Gromacs from:

http://mackerell.umaryland.edu/charmm_ff.shtml

However, I cannot connect to it in the last 10 days. Does anybody have any idea 
what's happening?

thanks a lot

Albert
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Re: [gmx-users] Alkane in water system simulation - TraPPE force field - Error: "Incorrect number of atomtypes for dihedral (4 instead of 2 and 4)"

[Peter Stern]

Hi,

I would start my removing the last unconnected line (l. 35) from forcefield.itp 
and try again.

Regards,
Peter

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Shantanu Singh 
[singhshantan...@gmail.com]
Sent: Monday, November 16, 2015 10:50
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Alkane in water system simulation - TraPPE force field - 
Error: "Incorrect number of atomtypes for dihedral (4 instead of 2 and 4)"

Hello!

Ignore the last mail.

So I am doing my B.Tech thesis on studying the diffusion coefficients of
alkanes at infinite dilution in water.
I am using TraPPE-UA model for alkanes and TIP4P/2005 representation for
water solvent. The problem is pretty simple but the simulations don't seem
to run.
I am currently working on ethane (C2H4).

When I try to run grompp for EM, I get the following error message -
*“Incorrect
number of atomtypes for dihedral (4 instead of 2 or 4)”. *
I figured there was something wrong with the topology file but nothing
seems out of place.


This is the link to the detailed error report and all other required files
for simulation:
*https://drive.google.com/file/d/0Bzfyv7uF7S2peGtOUEI0SExSdkU/view?usp=sharing
*


The command line I am using is :

grompp -f minim.mdp -c ethane.gro -p ethane.top -o em.tpr


It would be great if you could find the time to have a look at it and help
me out.


Thank you

--
Regards

Shantanu Singh
Senior Undergraduate
IIT Delhi
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Re: [gmx-users] Problem with GROMACS simulation

[Peter Stern]

Dear Shantanu,

As Erik already told you, your attachments aren't accepted by the list so 
nobody can see them.
You need to download your files to some public place where everyone can access 
them if they want, e.g. Dropbox, etc.
Without looking at the relevant files, nobody can possibly help your with your 
problem, because nobody can see what it is.
Also, it would be much more useful to give a more descriptive "Subject" to you 
"problem" if you can.

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
Shantanu Singh
Sent: Sunday, November 15, 2015 7:20 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem with GROMACS simulation

How do i get help regarding my simulations?

I am working on an alkane system using TraPPE force field. There is some issue 
which I can't figure out how to solve.



On Sat, Nov 14, 2015 at 9:54 PM, Erik Marklund 
wrote:

> Hi,
>
> I don’t think attachments are accepted on the mailing list.
>
> Kind regards,
> Erik
>
> > On 14 Nov 2015, at 15:32, Shantanu Singh 
> wrote:
> >
> > Hello!
> >
> > I am a Senior undergraduate at IIT delhi, India. I have trying to
> simulate
> > a system of alkanes in water with the ultimate aim of determining 
> > their diffusion coefficients.
> >
> > So, when I'm trying to run a simulation, it gives an error. A copy 
> > of the error report has also been attached herein along with all 
> > other files involved in the simulation.
> >
> > I would be really grateful if you could find the time to take a look 
> > at them and help me out. This project is an essential part of my 
> > bachelors
> and
> > is very important to me.
> >
> >
> > Thank you.
> >
> > --
> > Regards
> >
> > Shantanu Singh
> > Senior Undergraduate
> > IIT Delhi
> > --
> > 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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>
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--
Regards

Shantanu Singh
Senior Undergraduate
IIT Delhi
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 139, Issue 34

[Peter Stern]

Hi,



All your links give me the following, so I can't see what errors you are 
getting:
403 Forbidden

JSP3/2.0.4



But, you don't have to renumber the atoms in your PDB file.  Gromacs ignores 
those numbers and uses its own numbers.  Otherwise, how could it deal with 
numbers over 99,999 which won't fit into the pdb file's I5 format for atom 
numbers?  And when pdb2gmx adds hydrogen atoms it obviously has to renumber the 
coordinates.  It is possible that by editing your pdb or gro files you are 
introducing errors, but I don't know.



Regards,

Peter Stern



-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of ???
Sent: Monday, November 09, 2015 8:55 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 139, Issue 34



Dear,

I did some operations on my pdb or gro format file, for example, I deleted some 
atoms randomly to mimic a hole, then I had to re-number atoms in the pdb or gro 
format file by my code. The re-new pdb or gro file like picture 1 LINK: 
http://d.picphotos.baidu.com/album/s%3D550%3Bq%3D90%3Bc%3Dxiangce%2C100%2C100/sign=81b1352c18178a82ca3c7fa5c63802b0/cefc1e178a82b90149070cd3758da9773812efac.jpg?referer=54bbeb0fafec8a134d0d63d04962&x=.jpg,

thengromacs given errors like below picture 2 LINK: 
http://e.picphotos.baidu.com/album/s%3D550%3Bq%3D90%3Bc%3Dxiangce%2C100%2C100/sign=aec123e3ce95d143de76e42643cbf33f/d833c895d143ad4b3d75892084025aafa50f06f3.jpg?referer=c2157104b51c87018fa186d66292&x=.jpg,

but, I wrote itp and n2t file actually and there were no errors when uesd in 
others pdb or gro format structure file below 9 atoms. I consulted pdb web, 
I found that pdb format file reset 100,000th atom`s number to zero, then I 
reset the 100,000th atom number to 0, it shows in below picture 3 LINK: 
http://h.picphotos.baidu.com/album/s%3D550%3Bq%3D90%3Bc%3Dxiangce%2C100%2C100/sign=2f6ce308ba3eb13540c7b7be9625d9ee/18d8bc3eb13533fa2ded5cceaed3fd1f40345bf3.jpg?referer=7d7df4241dd5ad6ef3ee50daa591&x=.jpg.

Gromacs given errors again when I run jobs showed in below picture 4 LINK: 
http://f.picphotos.baidu.com/album/s%3D550%3Bq%3D90%3Bc%3Dxiangce%2C100%2C100/sign=711787ced41b0ef468e8985bedff20e7/7c1ed21b0ef41bd578bb271457da81cb38db3d62.jpg?referer=ace4f085b519ebc4996f42a97b21&x=.jpg.

Thanks a lot.

> Message: 5

> Date: Sun, 08 Nov 2015 09:14:39 +

> From: Mark Abraham mailto:mark.j.abra...@gmail.com>>

> To: gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>

> Subject: Re: [gmx-users] How to build a correct structure file beyond

>  9 atoms using pdb or gro extend format ?

> Message-ID:

>  
> mailto:CAMNuMAS=_dcwbjeh1s9+z62kz9h6vhlmq9yf1bu8jczfk9h...@mail.gmail.com>>

> Content-Type: text/plain; charset=UTF-8

>

> Hi,

>

> What errors?

>

> Mark

>

> On Sun, 8 Nov 2015 04:33 ??? 
> mailto:tianhuiquan0...@126.com>> wrote:

>

> > Dear all,

> > I worte itp file and n2t file of myself, and went some runs, gromacs

> > done well when I built a pdb or gro extend format structure file

> > contained less than 9 atoms, but gromacs will given errors when

> > numbers of atoms are beyond 9 in above structure file. I

> > consulted pdb web, and  found that pdb format file reset the

> > 100,000th atom's number to 0, then I did same way as pdb, but

> > gromacs given errors again, how should I do to correct my structure file?

> > Thanks in advance.

> > --

> > Gromacs Users mailing list

> >

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> >

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> End of gromacs.org_gmx-users Digest, Vol 139, Issue 34

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Re: [gmx-users] Fwd: OPLA

[Peter Stern]

For the delta carbon in the ring: CA alpha, CB beta, CG gamma, etc.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
Mehrnoosh Hazrati
Sent: Sunday, November 08, 2015 10:06 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Fwd: OPLA

Dear all,


what does "CD C in Trp" in OPLS atomtype list stand for?

Thank you in advance
Mehrnoosh


--
**
 Mehrnoosh Kh. Hazrati 
 PhD Candidate of Physical Chemistry,Tarbiat Modares University,Tehran, 
Iran 
 *** Phone : +989123436300 ***
*** Mail : mehrnoosh.hazr...@modares.ac.ir  ***
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Re: [gmx-users] Adding ion to force field

[Peter Stern]

Just guessing here but maybe you need to also add YB to the atomtypes.atp file.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Irem 
Altan
Sent: Wednesday, October 21, 2015 4:23 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Adding ion to force field

Thanks, leaving out .ff worked!

I’m still having a bit of trouble using the resulting .gro and .top files, 
though. I’m trying to create an executable that adds ions to the box, with the 
command

grompp -f ions.mdp -c box_h2o.gro -o ions.tpr -p topol.top

which gives me the error

Fatal error:
Syntax error - File ffnonbonded.itp, line 1 Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes

All I did was to add a line to the end of [atomtypes] with the info for the new 
ion:

YB  70 173.040.  A   1.65600e+00  4.0e-02

What could be the problem?

Best,
Irem

On Oct 21, 2015, at 2:03 AM, Peter Stern 
mailto:peter.st...@weizmann.ac.il>> wrote:

Or leave out the .ff:
pdb2gmx -f 1ytt_refine_001.pdb -ff amber99sb -o box.gro -p topol.top

Peter

-Original Message-
From: 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se<mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se>
 [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Wednesday, October 21, 2015 4:50 AM
To: gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>
Subject: Re: [gmx-users] Adding ion to force field



On 10/20/15 7:19 PM, Irem Altan wrote:
Hi,

I am trying to add an ion to amber99sb.ff. For this, I copied the amber99sb.ff 
folder to the folder I’m working in, and I also copied residuetypes.dat into 
the same directory. However, when I do pdb2gmx -f 1ytt_refine_001.pdb -ff 
amber99sb.ff -o box.gro -p topol.top, I get an error saying Could not find 
force field 'amber99sb.ff' in current directory, install tree or GMXDATA path.

Try selecting interactively, not using -ff.

-Justin

I am using GROMACS 4.6.5. My working folder looks something like:

1ytt_refine_001.pdb  nvt.mdp   residuetypes.dat 
  topol.top
amber99sb.ff posre_Protein_chain_A.itp 
topol_Protein_chain_A.itp  posre_Protein_chain_B.itp  topol_Protein_chain_B.itp

and the contents of amber99sb.ff  are:

aminoacids.arnaminoacids.r2b  dna.arn  ffbonded.itp gbsa.itp  rna.r2b   
tip3p.itpurea.itp
aminoacids.c.tdb  aminoacids.rtp  dna.hdb  ffnonbonded.itp  ions.itp  rna.rtp   
tip4pew.itp  watermodels.dat
aminoacids.hdbaminoacids.vsd  dna.r2b  forcefield.doc   rna.arn   spce.itp  
tip4p.itp
aminoacids.n.tdb  atomtypes.atp   dna.rtp  forcefield.itp   rna.hdb   spc.itp   
tip5p.itp

I only modified ffbonded.itp ions.itp atomtypes.atp  within the force field 
folder, and also residuetypes.dat in the working folder. What could be the 
problem?

Best,
Irem


--
==

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

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

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

==
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Re: [gmx-users] Adding ion to force field

[Peter Stern]

Or leave out the .ff:
pdb2gmx -f 1ytt_refine_001.pdb -ff amber99sb -o box.gro -p topol.top

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Wednesday, October 21, 2015 4:50 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Adding ion to force field



On 10/20/15 7:19 PM, Irem Altan wrote:
> Hi,
>
> I am trying to add an ion to amber99sb.ff. For this, I copied the 
> amber99sb.ff folder to the folder I’m working in, and I also copied 
> residuetypes.dat into the same directory. However, when I do pdb2gmx -f 
> 1ytt_refine_001.pdb -ff amber99sb.ff -o box.gro -p topol.top, I get an error 
> saying Could not find force field 'amber99sb.ff' in current directory, 
> install tree or GMXDATA path.

Try selecting interactively, not using -ff.

-Justin

> I am using GROMACS 4.6.5. My working folder looks something like:
>
> 1ytt_refine_001.pdb  nvt.mdp   residuetypes.dat   
> topol.top
> amber99sb.ff posre_Protein_chain_A.itp 
> topol_Protein_chain_A.itp  posre_Protein_chain_B.itp  
> topol_Protein_chain_B.itp
>
> and the contents of amber99sb.ff  are:
>
> aminoacids.arnaminoacids.r2b  dna.arn  ffbonded.itp gbsa.itp  rna.r2b 
>   tip3p.itpurea.itp
> aminoacids.c.tdb  aminoacids.rtp  dna.hdb  ffnonbonded.itp  ions.itp  rna.rtp 
>   tip4pew.itp  watermodels.dat
> aminoacids.hdbaminoacids.vsd  dna.r2b  forcefield.doc   rna.arn   
> spce.itp  tip4p.itp
> aminoacids.n.tdb  atomtypes.atp   dna.rtp  forcefield.itp   rna.hdb   spc.itp 
>   tip5p.itp
>
> I only modified ffbonded.itp ions.itp atomtypes.atp  within the force field 
> folder, and also residuetypes.dat in the working folder. What could be the 
> problem?
>
> Best,
> Irem
>

--
==

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

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

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

==
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Re: [gmx-users] distance between two index groups

[Peter Stern]

Hi Sabine,

Looks like you left out keyword group, i.e.:
gmx distance -n index.ndx -select 'com of group "A" plus com of group "B"' 

so:
gmx distance  -f test.xtc -s test.tpr -oall -n test.ndx   -select 'com of group 
"group1" plus com of group "group2"'

Peter Stern

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Sabine 
Reißer
Sent: Tuesday, September 01, 2015 4:52 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] distance between two index groups

Hi,

I want to calculate the distance over time between the COMs of two index 
groups. With g_dist, this used to be possible with the option -com, and an 
index file with the two groups between which the distance should be calculated. 
How can I do the same with the new version, now called gmx distance?

I checked "Tool changes for 5.0" on the website 
(http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0), and tried
gmx distance  -f test.xtc -s test.tpr -oall -n test.ndx   -select 'com 
of "group1" plus com of "group2"'
with test.ndx:
[ group1 ]
  1 2 3
[ group2 ]
4 5 6

and I get
Error in user input:
Invalid command-line options
   In command-line option -select
 In keyword 'com'
   In parameter 'of'
 invalid value
 invalid selection 'com of "group1" plus com of "group2"'



I'd be glad if someone could help.

Cheers
Sabine


--
Dr. Sabine Reißer
Theoretical Chemical Biology
Institute of Physical Chemistry
Karlsruhe Institute of Technology

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Re: [gmx-users] Impact of ignoring hydrogens

[Peter Stern]

Dear Suniba,

Matej is correct, but doing that can be quite tiresome.  Easier I believe to 
just map the unrecognized names in the arn file 
($GMXDATA/top/ffname/aminoacids.arn

Atom renaming database
Force fields often use atom names that do not follow IUPAC or PDB convention. 
The .arn
database is used to translate the atom names in the coordinate file to the 
force field names. Atoms
that are not listed keep their names. The file has three columns: the building 
block name, the old
atom name, and the new atom name, respectively.

Regards,
Peter Stern


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Repic 
Matej
Sent: Monday, August 31, 2015 4:04 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Impact of ignoring hydrogens

Dear Suniba,

The -ignh flag of pdm2gmx removes all the hydrogens from the pdb file and then 
adds them according to simple geometric rules. This should be fine for most 
hydrogens except for the exchangable protons of acidic and basic residues, 
where the algorithm quite possibly will not protonate all residues the same as 
in the NMR structure. Strictly, it is not necessary to remove the experimental 
data to make the simulation run, but it does make it more tedious.

The problems with pdb2gmx arise because the naming of H atoms in forcefield 
rtp/hbd files is not the same as in the pdb, thus you get quite a lot of 
errors. The solution is rather straighforward -> rename the hydrogens in your 
pdb to they match those from $GMXDATA/top/ffname/aminoacids.rtp. How you go 
about renaming efficiently is an entirely different thing.

Best,

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

--






On 8/31/15, 14:15, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf 
of su"  wrote:

>Hello All
>I am doing protein ligand MD to view the interactions and effect of 
>ligand on protein structure. However the NMR structure of protein 
>encountered some warnings and considering that, i ignored hydrogens by 
>-ignh. I believe that the hydrogen bonding might reduce due to this 
>action. Is that true? Can anyone please clear me what happens after the 
>application of -ignh.
>Thank You
>Suniba
>
>Sent from my iPhone
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Re: [gmx-users] How do I calculate the difference between two energy values?

[Peter Stern]

Indeed:
Sqrt(0.23**2+1.31**2)=1.33

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Johnny 
Lu
Sent: Thursday, August 27, 2015 3:31 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] How do I calculate the difference between two energy 
values?

Let x(t) be coulomb decoupling at time t.
Let y(t) be VdW decoupling at time t.

I guess the most safe way to get the answer is:
calculate z(t) = x(t) + y(t)
then, calculate standard deviation of z(t).

If x(t) and y(t) are independent and both x(t) and y(t) are normally 
distributed, then I guess using the error propagation rule is fine.
(https://en.wikipedia.org/wiki/Sum_of_normally_distributed_random_variables)



On Tue, Aug 25, 2015 at 2:15 PM, Peter Stern 
wrote:

> I believe that this is a statistics question and not a gromacs 
> question :-).
>
> 51.4 +/- 1.33 kJ/mol
>
> Sent from my iPad
>
> > On 25 באוג׳ 2015, at 14:44, minky son  wrote:
> >
> > Dear GROMACS users,
> >
> > I have been studying free energy calculation in Justin tutorial.
> >
> > I performed VDW decoupling and coulomb decoupling simulations separately.
> >
> > I obtained the free energy values for each simulation using gmx bar.
> >
> > coulomb decoupling simulation = 60.88 +/- 0.23 kJ/mol VDW decoupling 
> > simulation= -9.48 +/- 1.31 kJ/mol
> >
> > So, I want to calculate the sum of the two energy values,
> >
> > specially the second term (51.4  +/- ???).
> >
> >
> > Please give me any advice to solve this.
> >
> > Regards,
> > --
> > Gromacs Users mailing list
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> > or
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Re: [gmx-users] How do I calculate the difference between two energy values?

[Peter Stern]

I believe that this is a statistics question and not a gromacs question :-).

51.4 +/- 1.33 kJ/mol

Sent from my iPad

> On 25 באוג׳ 2015, at 14:44, minky son  wrote:
> 
> Dear GROMACS users,
> 
> I have been studying free energy calculation in Justin tutorial.
> 
> I performed VDW decoupling and coulomb decoupling simulations separately.
> 
> I obtained the free energy values for each simulation using gmx bar.
> 
> coulomb decoupling simulation = 60.88 +/- 0.23 kJ/mol
> VDW decoupling simulation= -9.48 +/- 1.31 kJ/mol
> 
> So, I want to calculate the sum of the two energy values,
> 
> specially the second term (51.4  +/- ???).
> 
> 
> Please give me any advice to solve this.
> 
> Regards,
> -- 
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Re: [gmx-users] submitting gmx cluster

[Peter Stern]

Or you can simply create a file, say "input" with an option on each line and 
then,
gmx something < input

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Lábas 
Anikó
Sent: Friday, July 31, 2015 11:53 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] submitting gmx cluster

Dear Gromacs Users,

I would like to submit my 'gmx cluster' job, but I don't know how can I define 
in my command line the following two options, which normally appear on the 
screen when I run gmx cluster on my head machine:
1. "Select group for least squares fit and RMSD calculation"
2. "Select group for output"

Can You tell me any suggestions?

Thank You in advance!

Aniko
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Re: [gmx-users] pdb2gmx error "residue not found in residue topology database"

[Peter Stern]

I never did that.


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of su
Sent: Wednesday, July 08, 2015 11:26 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] pdb2gmx error "residue not found in residue topology 
database"

How you converted the gaussian file into .pdb? Because once i did the same and 
suffered from some missing co ordinates. 

Sent from my iPhone

> On 08-Jul-2015, at 11:16 pm, Peter Stern  wrote:
> 
> Look at the file: residuetypes.dat in the ../top/ directory of your 
> installation.
> It lists all the residue names and more.
> 
> Peter Stern
> Weizmann Institute
> 
> Sent from my iPad
> 
>> On 8 ביולי 2015, at 17:45, Hamisu Aliyu Mohd  
>> wrote:
>> 
>> 
>> Dear gmx-users,
>> 
>> I am really new in this field of endeavour and I am trying investigate the 
>> solubility of peptides in organic solvents, I built a simple tripeptide 
>> (gly-gly-gly) using Gaussian 5.0 and I convert the output file(.out) to 
>> .pdb. I am now trying to use pdb2gmx tool to generate topology for my 
>> peptide using GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) I was 
>> promoted with an error "residue not found in residue topology database” I 
>> checked  GROMACS website at http://www.gromacs.org/Documentation/Errors I 
>> learned the residue must have the same name as in the force field, please I 
>> don’t know the naming convention of this force field please HELP.
>> 
>> Thanks 
>> Ali H.
>> Department of Chemistry
>> University Dutse
>> 
>> -- 
>> 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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Re: [gmx-users] pdb2gmx error "residue not found in residue topology database"

[Peter Stern]

Look at the file: residuetypes.dat in the ../top/ directory of your 
installation.
It lists all the residue names and more.

Peter Stern
Weizmann Institute

Sent from my iPad

> On 8 ביולי 2015, at 17:45, Hamisu Aliyu Mohd  wrote:
> 
> 
> Dear gmx-users,
> 
> I am really new in this field of endeavour and I am trying investigate the 
> solubility of peptides in organic solvents, I built a simple tripeptide 
> (gly-gly-gly) using Gaussian 5.0 and I convert the output file(.out) to .pdb. 
> I am now trying to use pdb2gmx tool to generate topology for my peptide using 
> GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) I was promoted with an 
> error "residue not found in residue topology database” I checked  GROMACS 
> website at http://www.gromacs.org/Documentation/Errors I learned the residue 
> must have the same name as in the force field, please I don’t know the naming 
> convention of this force field please HELP.
> 
> Thanks 
> Ali H.
> Department of Chemistry
> University Dutse
> 
> -- 
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Re: [gmx-users] Invalid full precision file format

[Peter Stern]

Thanks,
Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Monday, June 29, 2015 3:02 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Invalid full precision file format



On 6/29/15 7:50 AM, Peter Stern wrote:
> I am using GROMACS v5.0.5.  After successfully generating a topology file and 
> trying to optimize the added H-atoms with Steepest Descents:
> mdrun -pin on -s 1AQ3_A.tpr -o 1AQ3_A.trj -x 1AQ3_A.xtc -g 
> 1AQ3_A_1.log -v -nocompact -nt 4
>
> I get the error (no Notes, no Warnings):
> Program mdrun, VERSION 5.0.5
> Source code file: 
> /share/apps/gromacs-5.0.5/src/gromacs/fileio/mdoutf.c, line: 137
>
> Software inconsistency error:
> Invalid full precision file format
>
> A while ago I tried restarting an energy mimimization with v5.0.4 using a 
> topology file generated with v4.5.4 and I got the same error.
> So I reran it using v4.5.4 and it worked fine.  But this run is 
> starting from scratch using v5.0.5, so obviously the error is not a result of 
> some v4.5-v5.0 Incompatibility (which in any case, I doubted before).  So 
> what could be causing this error?
>

"Full precision format" refers to the trajectory; obsolete file formats like 
.trj have been removed.  Use .trr instead.

-Justin

--
==

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

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

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

==
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[gmx-users] Invalid full precision file format

[Peter Stern]

I am using GROMACS v5.0.5.  After successfully generating a topology file and 
trying to optimize the added H-atoms with Steepest Descents:
mdrun -pin on -s 1AQ3_A.tpr -o 1AQ3_A.trj -x 1AQ3_A.xtc -g 1AQ3_A_1.log -v 
-nocompact -nt 4

I get the error (no Notes, no Warnings):
Program mdrun, VERSION 5.0.5
Source code file: /share/apps/gromacs-5.0.5/src/gromacs/fileio/mdoutf.c, line: 
137

Software inconsistency error:
Invalid full precision file format

A while ago I tried restarting an energy mimimization with v5.0.4 using a 
topology file generated with v4.5.4 and I got the same error.
So I reran it using v4.5.4 and it worked fine.  But this run is starting from 
scratch using v5.0.5, so obviously the error is not a result of some v4.5-v5.0
Incompatibility (which in any case, I doubted before).  So what could be 
causing this error?

Thanks,
Peter Stern
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Re: [gmx-users] Does Gromacs take advantage of ECC memory?

[Peter Stern]

Dear Andrew,

ECC is Error Correction Code for the memory and is not related to you 
application.
For a single-user workstation, you generally don't need the ECC.  It is more 
important in servers.
Not every motherboard supports ECC and most desktop motherboards do not, so if 
you do get it, 
you should be sure that your motherboard (not your app) can utilize ECC memory.

Peter Stern
Weizmann Institute of Science

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Andrew 
DeYoung
Sent: Tuesday, June 23, 2015 6:36 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Does Gromacs take advantage of ECC memory?

Hi,

I'm looking into a workstation which I will use to run some Gromacs 
simulations.  I'm a chemist, not a computer person, so I'm not very well-versed 
in computer hardware.  I have the option of getting non-ECC or ECC memory, with 
the ECC being at extra cost.  In asking around about whether I need ECC, I've 
been advised to "research your simulation apps and see if they can take 
advantage of ECC."

I don't see ECC mentioned in the manual.  Does Gromacs take advantage of ECC?  
The simulations I will be running will not be terribly large: on the order of 
~10,000 atoms for a few tens of ns.  My system will likely have 8 cores.

Thanks so much for your time.

Andrew DeYoung
Carnegie Mellon University

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Re: [gmx-users] Get pdb2gmx not to treat the first nucleotide in a chain as 5'

[Peter Stern]

Even though it's called aminoacids.n.tdb?  Or a different name, e.g. 
nucleicacids.n.tdb?
One problem is that I eventually have to deal with tens, maybe hundreds of 
complexes.  
Some, of course, will have the normal 5' nucleotide.  Will I be able to choose 
the appropriate n.tdb file for each case
or will I have to copy the appropriate one to my run directory each time?  I 
guess the latter. 

Thanks,
Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Monday, June 22, 2015 9:39 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Get pdb2gmx not to treat the first nucleotide in a 
chain as 5'



On 6/22/15 2:36 PM, Peter Stern wrote:
> I have a chain of RNA in complex with a protein.
> The pdb file is missing the first two nucleotides and starts with the third 
> including the PO2 group.
> pdb2gmx identifies this as the 5' terminal nucleotide and tries to create the 
> topology from rna.rtp using RA5 as the "residue" type.
> Thus it  doesn't like the fact that the coordinates contain a P atom and 
> fails.  I would like to avoid removing the coordinates for PO2.
> How can I get pdb2gmx to treat the first (and last in other cases) nucleotide 
> as a "normal" residue?
> Simply changing the name of the residue from A to RA does not work.
>

You'll need to create an entry in the .n.tdb file that specifies a 5'-phosphate 
cap.

-Justin

--
==

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

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

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

==
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[gmx-users] Get pdb2gmx not to treat the first nucleotide in a chain as 5'

[Peter Stern]

I have a chain of RNA in complex with a protein.
The pdb file is missing the first two nucleotides and starts with the third 
including the PO2 group.
pdb2gmx identifies this as the 5' terminal nucleotide and tries to create the 
topology from rna.rtp using RA5 as the "residue" type.
Thus it  doesn't like the fact that the coordinates contain a P atom and fails. 
 I would like to avoid removing the coordinates for PO2.
How can I get pdb2gmx to treat the first (and last in other cases) nucleotide 
as a "normal" residue?
Simply changing the name of the residue from A to RA does not work.

Thanks,
Peter Stern

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