Re: [gmx-users] Best Force Field for a Membrane Protein

[francesco oteri]

Hi Anirban,
as far as I know the best force-field for membrane protein system is
Charm36: it uses Charm27 for proteins but an improved parametrization for
membrane lipids.
I don't know if the lipids part has been already ported in gromacs format,
but is a trivial task you can do in 1-2 days.

Francesco

Il giorno 19 aprile 2012 08:32, Anirban Ghosh  ha scritto:

> Hi ALL,
>
> When running a membrane protein (say GPCR) in a lipid bilayer (say POPC or
> DPPC etc.) which according to your experience is the most suited
> force-field in GROMACS that best retains the 7TM / secondary structures of
> the protein over long simulations? I have tried running with ff53a6 (as
> suggested in Justin's tutorial), but find that the helices in the bilayer
> tend to lose their helicity over time and turns into coils. ff43a2 seems to
> do the job somewhat better by retaining the helicity. Will ff43a1 work even
> better as the principle aim is to observe changes in the protein without
> losing its secondary structures? Your experience please.
> Thanks a lot in advance.
>
>
> Regards,
>
> Anirban
>
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Re: [gmx-users] PLUMED plugin in gromacs for protein system

[andrea spitaleri]

Hi Neeru,
this is an issue for the plumed mailing list. Try there.

http://sites.google.com/site/plumedweb/home

regards

and

On 04/19/2012 07:16 AM, neeru sharma wrote:

Dear gromacs users,

I am a gromacs user and need some help regarding the implementation of PLUMED 
plugin in gromacs.

I am simulating a system containing Protein-Mg-GDP and Protein-Mg-GTP using 
Gromacs which is a 166
residue protein+mg+GTP/GDP complex. I have already carried out classical MD 
simulation for the
Protein-Mg-GDP complex. Then, I replaced GDP with GTP in the complex and now 
have to analyse the
structural changes in the Protein-Mg-GTP complex during the simulation. I tried 
to perform classical
MD simulation for the Protein-Mg-GTP complex too. But, as GDP to GTP state 
transition is a
millisecond time-scale event, through classical MD, it seems practically 
impossible to achieve this
time-scale transition.


I was looking for the methods available in gromacs that can accelerate this 
event. I came across the
PLUMED plugin. I have some queries with respect to the above matter.

1) Can we manually specify simulation length when performing the simulation, 
that we want to finish
the simulation in the given specified time duration?
2) How can we specify reaction coordinates (Eg: The RMSD with the desired 
output state, Specific
H-bonding or distance pattern etc) for the simulation, as I already have the 
crystal structure
available with me for the Protein-Mg-GTP complex (output state desired to be 
achieved with the
simulation).

As, I am new to gromacs, can you please help me regarding the above mentioned 
matter, usage of
plumed plugin for protein system and how it can be approached with my system?


Any help will be highly appreciated.

Thanks in advance

Regards,

Neeru


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Re: [gmx-users] Re: Simulation in the high temperature conditions

[Mark Abraham]

On 19/04/2012 4:55 PM, James Starlight wrote:

Justin,


I've tested default disres applied to my protein under high 
temperature condiitions.


I've observed that default disre_dist as well as its values up to 0.3 
nm in general prevent destabilisation of my protein under non-native 
conditions allowing some dynamics of the restrained regions ( I've not 
used disre_frac in all this experiments). But starting from the values 
of 0.5 nm my protein was perturbed again.


So the remained questions are

1) Firstly  I'd like to test different cutoff radii for the 
increasing\decreasing number of disres but I didnt know how exactly 
define this value more accuracy ( previously I've used such cutoff 
radius for normal mode analysis of such protein ( in thact case Rc 
define contacts  between C-alpha atoms ) where the value of 0.8-1 nm 
gave me good results).


2) My protein consist of some internal water mollecules wich I've 
defined explicitly as the separate group (I've coppied coordinates of 
such waters from the X-ray structure ).  During dynamics RUN I've 
noticed that some of this waters were moved out from receptor to the 
SOL layer and only several waters remined in the bounded state with 
the interoiour of my protein.


Diffusion in and out of receptors is physical - you may not want to 
prevent that. At high temperatures the rate of diffusion will increase, 
and this is yet another problem with your attempted approach.


How I could specify T_couple and COM groups for such internal waters 
most accyracy?


COM removal is not for preventing a group of atoms from moving. Maybe a 
COM virtual site with a position restraint would achieve that, but if 
you really need to keep some water in the receptor, you need to put 
position restraints on those waters (and pray that your results mean 
something and people have a reason to believe you).


Mark

I've tried to define it as the part of SOL_Ions layer as well as in 
the common group with the protein for both the T_coupling and COM but 
I have not noticed any difference between that simulations.



Thanks for help again,


James

16 ?? 2012 ?. 18:09  Justin A. Lemkul > ???:




James Starlight wrote:

Justin,


Thank you for explanation. Tomorrow I'll try to check results
of simulation with the disres applied with its default values
as well as with narrower -disre_dist values ( ignorring
-disre_frac option at all )  and post here results of such
simulations.


1) The cut-off distance wich I've specified was defined with
the genrest comand with the -cutoff 1.0 flag. Finally all
restrains were apllied on the backbone atoms of alpha helices
of the Transmembrane domain of my protein wich I've defined in
the index.ndx file. So all loops of my protein were
not-restrained at all.


Ah, I see now.


Also I have some small  question about size of output edr
file. I've noticed that size of this files of such simulations
 (with the disres applied as well as with the -pd flag ) is a
very big ( 10-15 gb) Why this occurs and how I could fix it?



There are energy terms associated with distance restraints.  They
cause the .edr file to get large very fast if you have a lot of
them.  You'll have to decrease nstenergy to make the files
smaller, or not use the restraints.


-Justin

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MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Extending run using tpbconv and mdrun

[D_Roy]

Hi,

I am trying to do a simulation of 10ns of protein in water. Due to the
limitations in my computer speed, I have decided to break it up in 5 days
with 2ns run per day.

For the first 2ns run I have used the commands:

mdrun -v -deffnm protein_previous

I went through the gromacs documentation and tried the following method to
do an extended run of 2ns after the first day:

tpbconv -s protein_previous.tpr -extend 2000 -o protein_next.tpr
mdrun -s protein_next.tpr -cpi protein_previous.cpt -cpo protein_next.cpt

It worked for the first extended simulation giving me the output files:

confout.gro ; ener.edr ; traj.xtc ; traj.trr ; md.log

When I try the same steps for 2ns for the third time with the commands:

tpbconv -s protein_next.tpr -extend 2000 -o protein_another.tpr
mdrun -s protein_another.tpr -cpi protein_next.cpt -cpo protein_another.cpt

It start from the beginning. 
>From the mailing lists, I could guess it may be that mdrun cannot find the
checkpoint file previous_next.cpt. But the filename is correct. So why is it
starting from the begining?

Would appreciate if someone can help me out.

Thanks.
Dipankar Roy

-
Research Assistant
Sikkim Manipal University DE

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Re: [gmx-users] Extending run using tpbconv and mdrun

[Mark Abraham]

On 19/04/2012 6:16 PM, D_Roy wrote:

Hi,

I am trying to do a simulation of 10ns of protein in water. Due to the
limitations in my computer speed, I have decided to break it up in 5 days
with 2ns run per day.

For the first 2ns run I have used the commands:

mdrun -v -deffnm protein_previous

I went through the gromacs documentation and tried the following method to
do an extended run of 2ns after the first day:

tpbconv -s protein_previous.tpr -extend 2000 -o protein_next.tpr
mdrun -s protein_next.tpr -cpi protein_previous.cpt -cpo protein_next.cpt

It worked for the first extended simulation giving me the output files:

confout.gro ; ener.edr ; traj.xtc ; traj.trr ; md.log

When I try the same steps for 2ns for the third time with the commands:

tpbconv -s protein_next.tpr -extend 2000 -o protein_another.tpr
mdrun -s protein_another.tpr -cpi protein_next.cpt -cpo protein_another.cpt

It start from the beginning.
> From the mailing lists, I could guess it may be that mdrun cannot find the
checkpoint file previous_next.cpt. But the filename is correct. So why is it
starting from the begining?


Look in the .log file for what mdrun thought about the (default) request 
for appending to previous output files.


Mark
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Re: [gmx-users] Extending run using tpbconv and mdrun

[Mark Abraham]

On 19/04/2012 6:16 PM, D_Roy wrote:

Hi,

I am trying to do a simulation of 10ns of protein in water. Due to the
limitations in my computer speed, I have decided to break it up in 5 days
with 2ns run per day.

For the first 2ns run I have used the commands:

mdrun -v -deffnm protein_previous

I went through the gromacs documentation and tried the following method to
do an extended run of 2ns after the first day:

tpbconv -s protein_previous.tpr -extend 2000 -o protein_next.tpr
mdrun -s protein_next.tpr -cpi protein_previous.cpt -cpo protein_next.cpt

It worked for the first extended simulation giving me the output files:

confout.gro ; ener.edr ; traj.xtc ; traj.trr ; md.log

When I try the same steps for 2ns for the third time with the commands:

tpbconv -s protein_next.tpr -extend 2000 -o protein_another.tpr
mdrun -s protein_another.tpr -cpi protein_next.cpt -cpo protein_another.cpt

It start from the beginning.
> From the mailing lists, I could guess it may be that mdrun cannot find the
checkpoint file previous_next.cpt. But the filename is correct. So why is it
starting from the begining?



 See also new example 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#section_1


Mark
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Re: [gmx-users] Re:WHAM question

[lloyd riggs]

 Original-Nachricht 
> Datum: Wed, 18 Apr 2012 10:49:00 -0400
> Von: "Justin A. Lemkul" 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] Re:WHAM question

> 
> 
> lloyd riggs wrote:
> >> When accusing the code of doing something wrong, "I don't know" isn't a
> >> >very good justification ;)  The contents of pullx.xvg are the COM
> >> >Acoordinates of the reference group on the axis or axes along which
> the
> >> >restraint was applied, followed by the distance between the reference
> and
> >> >pulled group, again along each axis.  In your case you should have the
> >> y->coordinate of the COM of the reference, and dY, which represents the
> >> >distance between the two groups along the y-axis only.  These values
> >> >should be easy to confirm with g_traj and g_dist.
> > 
> > My pullx.xvg file, as I think I mentioned, prints the refernce
> coordinates
> > and the coordinates of the COM of the pulled group.  I can in a spread
> sheet
> > (minus the reformating 10 times) just make a column of the dY.
> > 
> > My question, do you or anyone know why it prints the reference and
> pulled COM
> > rather than the pulled COM and dY?  Can somone compile something that
> way, or
> > is it some bug or maybe just something to do with the N Y N vs. N N Y
> > pulling?
> > 
> 
> The content of pullx.xvg (according to the headers and the explanations I
> have 
> seen) is indeed the COM of the reference and dY, not the coordinate(s) of
> the 
> pulled group.  Does g_dist contradict these assertions?  I am basing my 
> knowledge on its contents based on the printed header and statements from
> the 
> developers, but if something has gone wrong here, it's an important
> (potential) 
> bug to fix.
> 
> -Justin
> 

Dear Justin,

I tried it once, yes g_dist contradicts it well and gives the actual distances 
dy between the COMs.  Also, If I (I did this weeks back) use I think g_analyze 
or the utility which gives coordinates, print out the Y coordinates for the COM 
of the pulled group and it is the secound column printed to the pullx.xvg file. 
 The Gromacs instillation has been taken ove by the Chem/Computer admin so they 
are now responsible for it.  I also have it on my home PC, but can only use 
auxillary analysis scripts as it would take 1 year to run something unless I 
ported things to openCL, which would probably take me personally XX years.  I 
think however I am the only one using Gromacs here except for a 1 or 2 times a 
year course from the chem departmentas the problem is only with the 
instillation here I dont know if it is a bug, or maybe an instillation problem, 
or something else (seems like only a 2 line get and print to file thing could 
do that though, or it skips the A-B=delta portion of
  the script which I have no clue where is located?)

Sincerely,

Stephan Watkins





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

[chip]

Dear Gromacs Users and Developers,

 

 

I'm trying to simulate a protein-ligand complex system using GROMACS 4.5.3
and Amber03 forcefield.

 

In this system, a carbocationic intermediate was used as ligand

 

 

C - C+ - C - C - O-PP (Carbocationic intermediate)

│

C

 

I tried to obtain topology file for intermediate molecule using ACPYPE

 

[Command: acpype -i intermediate.mol2 -n -2]

 

But, ACPYPE didn't recognize the carbocation

 

 

So, I firstly obtained topology file for substrate molecule

 

 

C = C - C - C - O-PP (Substrate: IPP)

│

C

 

[Command: acpype -i IPP.mol2 -n -3]

 

 

Then, I tried to modify [atomtypes] in IPP.itp file by adding atomtype for
carbocationic carbon

 

But, I couldn't do this

 

 

[ atomtypes ] <--- IPP.itp
===

 

;name   bond_type mass charge   ptype   sigma epsilon
Amb

 c3   c3  0.0  0.0   A 3.39967e-01   4.57730e-01 ;
1.91  0.1094  ; single bonded carbon

 c2   c2  0.0  0.0   A 3.39967e-01   3.59824e-01 ;
1.91  0.0860  ; double bonded carbon

 os   os  0.0  0.0   A 3.1e-01   7.11280e-01 ;
1.68  0.1700

 p5   p5  0.0  0.0   A 3.74177e-01   8.36800e-01 ;
2.10  0.2000

 oo   0.0  0.0   A 2.95992e-01   8.78640e-01 ;
1.66  0.2100

 h1   h1  0.0  0.0   A 2.47135e-01   6.56888e-02 ;
1.39  0.0157

 hc   hc  0.0  0.0   A 2.64953e-01   6.56888e-02 ;
1.49  0.0157

 ha   ha  0.0  0.0   A 2.59964e-01   6.27600e-02 ;
1.46  0.0150


=

 

how to obtain sigma and epsilon values for carbocationinc carbon ?

 

I've read the manual, but I'm still none the wiser

 

I'am a lack of knowledge about this

 

Please kindly give some suggestions and comments 

 

Is it right this way to make the topology file for carbocationic
intermediate ?

 

 

 

Thanks,

 

 

Chanin Park

 

---

Department of Biochemistry and Division of Applied Life Science

Gyeonsang National University (GNU)

Republic of Korea (South Korea)

Email: c...@bio.gnu.ac.kr

---

 

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Re: [gmx-users] Extending run using tpbconv and mdrun

[Erik Marklund]

Hi,

Why not just run the simulation for a limited time (as in real time)? E.g. 
mdrun ... -maxh 8 if you want it to run overnight for 8 hours. If the computer 
you are using is not used for other tasks, then there would be no reason at all 
to spit the simulation in parts. Even if the simulation has not completed the 
number of steps dictated by the tpr file you can still analyze the results 
after 2 ns of simulation. It sounds like your strategy creates unnecessary work 
for you.

Best,

Erik

19 apr 2012 kl. 10.16 skrev D_Roy:

> Hi,
> 
> I am trying to do a simulation of 10ns of protein in water. Due to the
> limitations in my computer speed, I have decided to break it up in 5 days
> with 2ns run per day.
> 
> For the first 2ns run I have used the commands:
> 
> mdrun -v -deffnm protein_previous
> 
> I went through the gromacs documentation and tried the following method to
> do an extended run of 2ns after the first day:
> 
> tpbconv -s protein_previous.tpr -extend 2000 -o protein_next.tpr
> mdrun -s protein_next.tpr -cpi protein_previous.cpt -cpo protein_next.cpt
> 
> It worked for the first extended simulation giving me the output files:
> 
> confout.gro ; ener.edr ; traj.xtc ; traj.trr ; md.log
> 
> When I try the same steps for 2ns for the third time with the commands:
> 
> tpbconv -s protein_next.tpr -extend 2000 -o protein_another.tpr
> mdrun -s protein_another.tpr -cpi protein_next.cpt -cpo protein_another.cpt
> 
> It start from the beginning. 
>> From the mailing lists, I could guess it may be that mdrun cannot find the
> checkpoint file previous_next.cpt. But the filename is correct. So why is it
> starting from the begining?
> 
> Would appreciate if someone can help me out.
> 
> Thanks.
> Dipankar Roy
> 
> -
> Research Assistant
> Sikkim Manipal University DE
> 
> --
> View this message in context: 
> http://gromacs.5086.n6.nabble.com/Extending-run-using-tpbconv-and-mdrun-tp4897317p4897317.html
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Re: [gmx-users] Best Force Field for a Membrane Protein

[Thomas Piggot]

Hi,

The CHARMM36 force field is already available, see the user 
contributions section on the GROMACS website.


As for the original question on which is "best", it is a hard question 
to answer. It really depends on what you need. For example, are you just 
looking at PC lipids in your membrane, or do you want to use lipids like 
PE, PG, etc. This may alter your choice of force field. Also be aware if 
you use an all-atom force field for your membrane (like CHARMM) your 
simulation will take substantially longer, but the protein model may be 
slightly better than one of the united-atom GROMOS force fields. You 
could also choose the combination of the united-atom Berger force field 
with an all-atom force field (OPLS or AMBER) for the protein. This seems 
like an attractive compromise but there has not been a huge amount of 
work looking at these combinations. You really will have to weigh up 
these different factors yourself and decide what is best for you. Also 
be aware that it is really important that once you have made the choice 
of force field, you use an appropriate set of simulation parameters for 
this force field.


As for your point about the GROMOS 53A6 force field, it is know that 
this force field can have problems with short helices unwinding and 
there has been an update of this force field (GROMOS 54A7) to try and 
address these problems. We have been using this force field with no such 
issues. You can download the force field files from the ATB website 
(http://compbio.biosci.uq.edu.au/atb/). This might be the simplest 
solution for you, as you will not need to change your structure file (so 
no need to re-insert your protein into the membrane).


Cheers

Tom

francesco oteri wrote:

Hi Anirban,
as far as I know the best force-field for membrane protein system is 
Charm36: it uses Charm27 for proteins but an improved parametrization 
for membrane lipids.
I don't know if the lipids part has been already ported in gromacs 
format, but is a trivial task you can do in 1-2 days.


Francesco

Il giorno 19 aprile 2012 08:32, Anirban Ghosh 
mailto:reach.anirban.gh...@gmail.com>> 
ha scritto:


Hi ALL,

When running a membrane protein (say GPCR) in a lipid bilayer (say
POPC or DPPC etc.) which according to your experience is the most
suited force-field in GROMACS that best retains the 7TM / secondary
structures of the protein over long simulations? I have tried
running with ff53a6 (as suggested in Justin's tutorial), but find
that the helices in the bilayer tend to lose their helicity over
time and turns into coils. ff43a2 seems to do the job somewhat
better by retaining the helicity. Will ff43a1 work even better as
the principle aim is to observe changes in the protein without
losing its secondary structures? Your experience please.
Thanks a lot in advance.


Regards,

Anirban

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Cordiali saluti, Dr.Oteri Francesco



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[gmx-users] Re: Extending run using tpbconv and mdrun

[D_Roy]

Thanks for the reply. 
About the log file, are you taking about the init_step? 

About the new documentation I understand the first two steps but don't get
the third step. Is mv a command or option of tpbconv? There is no such thing
in online manual.

-
Research Assistant
Sikkim Manipal University DE

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[gmx-users] Re: Extending run using tpbconv and mdrun

[D_Roy]

Hi, 
My computer can only manage 2ns in 8 hours. I need a 10ns of simulation run
for which I have to break up the simulation. You have mentioned using maxh
option to run the simulation. I read in the mailing list it can be used to
extend a simulation run and is a better option than tpbconv.

Can you help me out as to how to use the maxh option to extend the
simulation?

I have performed the first step with mdrun -v -deffnm protein_previous

Now how will I extend this?

Thanks,
Dipankar Roy

-
Research Assistant
Sikkim Manipal University DE

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Re: [gmx-users] pdb2gmx error

[Justin A. Lemkul]

Bishwajit Das wrote:
Hi, i attached my pdb file,please check it... fixed.pdb is after fixing 
it into what if server and actin.pdb is original pdb file.The exact 
error is




The coordinate file is not in an order that Gromacs can work with.  It is 
arranged such that various groups of atoms are continuous rather than residues. 
   pdb2gmx will be unable to work with this file unless you re-order it so that 
the residues are sequential.


-Justin


Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff

Opening force field file 
/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b

Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b
Reading fixed.pdb...
Read 'DUMMY', 2878 atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
WARNING: Chain identifier 'A' is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
There are 2 chains and 0 blocks of water and 73 residues with 2878 atoms

  chain  #res #atoms
  1 'A'  2659   2867 
  2 'A' 1 11 



WARNING: there were 0 atoms with zero occupancy and 8 atoms with
 occupancy unequal to one (out of 2878 atoms). Check your pdb file.

Opening force field file 
/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp

Atomtype 1
Reading residue database... (amber99sb-ildn)
Opening force field file 
/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp

Residue 93
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp
Residue 109
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp
Residue 125
Sorting it all out...
Opening force field file 
/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb

Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb
Opening force field file 
/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb
Opening force field file 
/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb


Back Off! I just backed up topol.top to ./#topol.top.6#
Processing chain 1 'A' (2867 atoms, 2659 residues)
There are 549 donors and 549 acceptors
There are 773 hydrogen bonds

---
Program pdb2gmx, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/kernel/hizzie.c, line: 270

Fatal error:
Incomplete ring in HIS40
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


On Tue, Apr 10, 2012 at 1:35 AM, Justin A. Lemkul > wrote:




Bishwajit Das wrote:

when i try to  pdb2gmx -f *.pdb -o *_processed.gro -water spce
command in my pdb file then i select  AMBER99SB-ILDN force field
(Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) this force
field but a error massage came.
the massage is following:

There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Identified residue GLU6 as a starting terminus.
Identified residue GLU6 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus GLU-6: NH3+
End terminus GLU-6: COO-
Checking for duplicate atoms

--__-
Program pdb2gmx, VERSION 4.5.4
Source code file:
/build/buildd/gromacs-4.5.4/__src/kernel/pgutil.c, line: 88

Fatal error:
Atom CG not found in residue seq.nr 
. 1 while adding atom


For more information and tips for troubleshooting, please check
the GROMACS
website at http://www.gromacs.org/__Documentation/Errors

---
 then i repair my protein with what if server as instruction
given in gromacs documentation...then i again run the above
process but still showing me a error massage.The massage was His
450 chain is not complete.How i overcome this problem..please
give me a suggestion.


The exact error message, copied and pasted from your terminal along
with any other relevant output, would be useful.  As it stands, the
output you posted suggests that you have a single amino acid (since
Glu-6 is both the start and end residue), but this is clearly not
the case with the error at hand if something is wrong with His-450.

No matter the case, the general solution is that the atom naming
must match that of the .rtp entry for the residue being processed.
 If this is not true, either you are missing atoms or have a naming
mismatch.  If the error arises due to a hydrogen atom, either use
-ignh to ignore H atoms in the

Re: [gmx-users] Re: Extending run using tpbconv and mdrun

[Erik Marklund]

-maxh is not about extending the simulation. What you do is that you start a 10 
ns simulation that write checkpoints at regular intervals. With the -maxh 
option you instruct mdrun to run a certain amount of time (e.g. 8 hours 
overnight) and the next time you start the simulation (e.g. the next evening) 
it will continue from the last checkpoint file. Thus there is no need for 
dividing your simulation in 2 ns chunks with separate tpr/trr/xtc/edr/log 
files, for mdrun will append further output to the existing files.

If you have already completed a 2 ns simulation and wish to extend it further I 
think that extending it to 10 ns and use the strategy outlined above is easier 
than splitting it into more parts. Note how unintuitive it is with a bunch of 
tpr files named protein_previous, protein_another, etc. There is little point 
in manually keeping track of what file belong to what part of the simulation 
when mdrun is capable of continuing form a cpt file ans appending the output to 
existing files.

Erik
 
19 apr 2012 kl. 12.02 skrev D_Roy:

> Hi, 
> My computer can only manage 2ns in 8 hours. I need a 10ns of simulation run
> for which I have to break up the simulation. You have mentioned using maxh
> option to run the simulation. I read in the mailing list it can be used to
> extend a simulation run and is a better option than tpbconv.
> 
> Can you help me out as to how to use the maxh option to extend the
> simulation?
> 
> I have performed the first step with mdrun -v -deffnm protein_previous
> 
> Now how will I extend this?
> 
> Thanks,
> Dipankar Roy
> 
> -
> Research Assistant
> Sikkim Manipal University DE
> 
> --
> View this message in context: 
> http://gromacs.5086.n6.nabble.com/Extending-run-using-tpbconv-and-mdrun-tp4897317p4897668.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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---
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Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
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[gmx-users] Re: Extending run using tpbconv and mdrun

[D_Roy]

Thanks for helping me out here. I'll redo my run with the -maxh option and
see how it goes.

-Dipankar Roy

-
Research Assistant
Sikkim Manipal University DE

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[gmx-users] Thole Potential

[Sai Janani Ganesan]

Hi,

I am trying to use Thole potential to implement polarization effects with
drudes. I know NAMD and CHARMM have clear protocols, but I am unable to
find much information on how it is implemented in Gromacs. Can someone tell
me where I can find an example file to understand the use of [polarization]
and [thole_polarization] in the topology file?

Thanks,
Sai
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[gmx-users] extra factor in PMF

[Gavin Melaugh]

Hi all

According to some references

1) J. Chem. Phys, 128, 044106, (2008)
 
2) Comparison of Methods to Compute the Potential of Mean Force

Daniel Trzesniak, Anna-Pitschna E. Kunz, Wilfred F. van Gunsteren Prof.
Article first published online: 28 NOV 2006
DOI: 10.1002/cphc.200600527



There is an extra factor that has to be taken into account when
calculating the PMF. This extra factor (2kTln(r)) results from the
transformation from the 3N Cartesian coordinates to 3N internal
coordinates. In the case of a reaction coordinate defined by a distance
r between two species the Jacobian (r*2sin(theta)) of the transformation
for 3D to  1D leads to an extra term in the PMF.
Therefore the true PMF should be

PMF(true) = PMF(g_wham) + 2kTln(r)


This extra factor is only significant at lower values of the reaction
coordinate. My question is; Does g_wham take this into account ?

Cheers

Gavin

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Re: [gmx-users] Re: Extending run using tpbconv and mdrun

[Mark Abraham]

On 19/04/2012 7:55 PM, D_Roy wrote:

Thanks for the reply.
About the log file, are you taking about the init_step?

About the new documentation I understand the first two steps but don't get
the third step. Is mv a command or option of tpbconv? There is no such thing
in online manual.


mv is a standard Unix command...

Mark
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[gmx-users] Re: : Extending run append

[lloyd riggs]

Dear All,

Another error here with Gromacs

The append from continuing runs does not work.  It complains that several files 
are missing.  When I try to give it the files in the working DIR or direct 
paths, it still gives the same complaint.

I woundered if such a thing could also be a compilation time error, or 
something else.

Sincerely,

Stephan Lloyd Watkins
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[gmx-users] g_nmeig & eigenfrequencies

[Yongchul Chung]

Hi all,

I've carried out the normal mode analysis on my system using g_nmeig
command, and from this, I have eigenfreq.xvg, eigenval.xvg, and
eigenvec.trr.

However, I was not aware that I can set the number of eigenvector/frequency
to be written on XVG files (default is 1 to 50 lowest), and now want to get
as many as I can without invoking g_nmeig command. This leads to 2
questions.

1. Is there a way to calculate eigenfreq, and eigenval from eigenvec.trr?

2. If there's none, is there a way to set "-last" flag that it will always
output all the frequency and vector values? I've tried "-1" but does not
work.

I'm using GROMACS 4.5.5.

Thanks,

Greg
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[gmx-users] (no subject)

[Nilesh Dhumal]

Hello,

 I am doing solvation dynamics for my system.
 I have system with diatomic (PA---NE)solute surrounded by water molecules.

 I am running simulation for two differcent cases.
 1. PA charge=0 and NE charge=0 : No charge on solute

 2. PA charge=+1 and NE charge=-1 : Charge on solute

For second case I am using rerun option to calculate the energy with
charge for same configuration.


grompp -f md.mdp  -c  solvent-bmi-pf6-128.pdb   -p 
solvent-bmi-pf6-128.top  -o md-rerun.tpr
/opt/mpich_intel/ch-p4/bin/mpirun -machinefile cp -np 2 
/usr/local/gromacs/bin/mdrun_mpi  -s md-rerun.tpr  -o md-rerun.trr -c
solvent-bmi-pf6-128.pdb -e md-rerun.edr -rerun md.trr  -g md-rerun.log


The total energy difference between change and neutal is large around ~350
kj/mole. It should be around 30 kJ /mole.


Can you tell why I getting large high energy differmece.


I using Gromacs VERSION 4.0.5.

NIlesh


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Re: [gmx-users] Re: : Extending run append

[Erik Marklund]

Could toy provide us with the full command line and listing the files in the 
directory you run from?

Erik

19 apr 2012 kl. 17.45 skrev lloyd riggs:

> 
> Dear All,
> 
> Another error here with Gromacs
> 
> The append from continuing runs does not work.  It complains that several 
> files are missing.  When I try to give it the files in the working DIR or 
> direct paths, it still gives the same complaint.
> 
> I woundered if such a thing could also be a compilation time error, or 
> something else.
> 
> Sincerely,
> 
> Stephan Lloyd Watkins
> -- 
> NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone!
>   
> Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a
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---
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
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[gmx-users] Writing out individual coordinates

[patrick wintrode]

Hi.

For each alpha carbon in my protein, I want to write out the x, y and z 
coordinates as separate time series.

If I use g_traj with the flags -oxt -x (or y orz) and -n along with an index 
file selecting the appropriate alpha carbon, will that do the trick? Does 
anyone know of a less cumbersome way of doing this?

Thanks.

Patrick L. Wintrode
University of Maryland School of Pharmacy
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Re: [gmx-users] Writing out individual coordinates

[Justin A. Lemkul]

patrick wintrode wrote:

Hi.

For each alpha carbon in my protein, I want to write out the x, y and z 
coordinates as separate time series.


If I use g_traj with the flags -oxt -x (or y orz) and -n along with an 
index file selecting the appropriate alpha carbon, will that do the 
trick? Does anyone know of a less cumbersome way of doing this?




You don't necessarily have to do each alpha carbon separately (though you could 
script all of it, which is relatively easy).  If you use the default C-alpha 
group, all of the chosen x/y/z coordinates are printed in order of the atom 
number, which can then be parsed with something like awk or perl.


-Justin

--


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


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Re: [gmx-users] Writing out individual coordinates

[Rodrigo Faccioli]

I believe BioPython project can help you. It load a PDB file and you have
methods which help you selecting atoms.

Please see [1]...

[1] http://biopython.org/wiki/Main_Page

Best regards,

--
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Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
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On Thu, Apr 19, 2012 at 5:25 PM, Justin A. Lemkul  wrote:

>
>
> patrick wintrode wrote:
>
>> Hi.
>>
>> For each alpha carbon in my protein, I want to write out the x, y and z
>> coordinates as separate time series.
>>
>> If I use g_traj with the flags -oxt -x (or y orz) and -n along with an
>> index file selecting the appropriate alpha carbon, will that do the trick?
>> Does anyone know of a less cumbersome way of doing this?
>>
>>
> You don't necessarily have to do each alpha carbon separately (though you
> could script all of it, which is relatively easy).  If you use the default
> C-alpha group, all of the chosen x/y/z coordinates are printed in order of
> the atom number, which can then be parsed with something like awk or perl.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
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Re: [gmx-users] Best Force Field for a Membrane Protein

[Peter C. Lai]

Define long simulations? CHARMM27/36 in the sub-100ns timescale works for us.

The following paper:
Vanni, S., Neri, M., Tavernelli, I., and Rothlisberger, U.: Predicting Novel 
Binding Modes of
Agonists to Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations. 
PLoS
Comput Biol 7, e1001053 (2011) 

Uses Amber99SB over 500-800+ns for their beta2-adrenergic receptor system.

On 2012-04-19 12:02:36PM +0530, Anirban Ghosh wrote:
> Hi ALL,
> 
> When running a membrane protein (say GPCR) in a lipid bilayer (say POPC or
> DPPC etc.) which according to your experience is the most suited
> force-field in GROMACS that best retains the 7TM / secondary structures of
> the protein over long simulations? I have tried running with ff53a6 (as
> suggested in Justin's tutorial), but find that the helices in the bilayer
> tend to lose their helicity over time and turns into coils. ff43a2 seems to
> do the job somewhat better by retaining the helicity. Will ff43a1 work even
> better as the principle aim is to observe changes in the protein without
> losing its secondary structures? Your experience please.
> Thanks a lot in advance.
> 
> 
> Regards,
> 
> Anirban

> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
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-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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[gmx-users] Units of density in the g_spatial output

[Andrew DeYoung]

Hi, 

Does anyone know what the units of density are in the output (Gaussian 98
cube format) of the spatial distribution function in g_spatial?  Is it a
number density or a mass density?  If it is a number density, then I would
guess that the units might be atoms/nm^3, since nm is the unit of length in
Gromacs.  If it is a mass density, then I would guess that the units might
be (atomic mass unit)/nm^3.

When I look in gmx_spatial.c, I see a line with the declaration "static
const double bohr=0.529177249;  /* conversion factor to compensate for VMD
plugin conversion... */" [line 55].  It seems that this value is in the
denominator in subsequent calculations [for example, lines 267-270].  I am
not sure what this means.  The comment in the code seems to imply that VMD
does it own processing of the cube file.  But when I asked on the VMD
mailing list, I got this response:

"The units are whatever the units of the data you loaded were. The values in
the isovalue slider correspond directly to the data values that the
associated VMD molfile plugin read from the input file, unless some kind of
unit conversion was done on the fly, but in the case of volumetric data,
none of the existing plugins do any unit conversions...  The reason the
units aren't specified is that many of the existing volumetric file formats
don't include any provision to label the units  in the file, and/or the
programs that generate the volumetric files don't  bother to write the units
even if the file format supports it. The units of the isovalue slider in VMD
are therefore directly related to the per-voxel scalar values stored in the
volumetric data file, e.g. a density value (not the cartesian coordinates,
not lengths, etc)."

Indeed, when I open a cube file that is output by g_spatial, I do not see
any units specified in the file (probably Gaussian98 does not support it).

Do you have any suggestions?

Thank you!

Andrew DeYoung
Carnegie Mellon University

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Re: [gmx-users] Re: : Extending run append

[Mark Abraham]

On 20/04/2012 1:45 AM, lloyd riggs wrote:

Dear All,

Another error here with Gromacs

The append from continuing runs does not work.  It complains that several files 
are missing.  When I try to give it the files in the working DIR or direct 
paths, it still gives the same complaint.

I woundered if such a thing could also be a compilation time error, or 
something else.


Not likely. User error or file system issue are the most likely 
explanations, but we have nowhere near enough information to help.


Mark
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[gmx-users] t-Butyl sulfinamide Stability

[Nancy]

Hello,

Does anyone know how stable sulfinamides are in vivo? Specifically,
molecules such as Ellman's t-butyl sulfinamide. How does their stability
compare to sulfoxides? Do they get oxidized in vivo?  Are they at least
stable in water?

Thanks in advance,
Nancy
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Re: [gmx-users] Writing out individual coordinates

[Tsjerk Wassenaar]

Hey :)

Why not just use trjconv to write a .pdb file? C-alpha atoms is
offered as standard group, and the resulting file can be easily
processed with sed/python.

Cheers,

Tsjerk

On Thu, Apr 19, 2012 at 10:47 PM, Rodrigo Faccioli
 wrote:
> I believe BioPython project can help you. It load a PDB file and you have
> methods which help you selecting atoms.
>
> Please see [1]...
>
> [1] http://biopython.org/wiki/Main_Page
>
> Best regards,
>
> --
> Rodrigo Antonio Faccioli
> Ph.D Student in Electrical Engineering
> University of Sao Paulo - USP
> Engineering School of Sao Carlos - EESC
> Department of Electrical Engineering - SEL
> Intelligent System in Structure Bioinformatics
> http://laips.sel.eesc.usp.br
> Phone: 55 (16) 3373-9366 Ext 229
> Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
> Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
>
>
> On Thu, Apr 19, 2012 at 5:25 PM, Justin A. Lemkul  wrote:
>>
>>
>>
>> patrick wintrode wrote:
>>>
>>> Hi.
>>>
>>> For each alpha carbon in my protein, I want to write out the x, y and z
>>> coordinates as separate time series.
>>>
>>> If I use g_traj with the flags -oxt -x (or y orz) and -n along with an
>>> index file selecting the appropriate alpha carbon, will that do the trick?
>>> Does anyone know of a less cumbersome way of doing this?
>>>
>>
>> You don't necessarily have to do each alpha carbon separately (though you
>> could script all of it, which is relatively easy).  If you use the default
>> C-alpha group, all of the chosen x/y/z coordinates are printed in order of
>> the atom number, which can then be parsed with something like awk or perl.
>>
>> -Justin
>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Best Force Field for a Membrane Protein

[Anirban Ghosh]

Hi ALL,

Thanks a lot for the replies.
By long simulation I mean 500 ns to 1000 ns. Has anybody tried with the
ff43a1 with any membrane protein?

Thanks,

Anirban

On Fri, Apr 20, 2012 at 3:26 AM, Peter C. Lai  wrote:

> Define long simulations? CHARMM27/36 in the sub-100ns timescale works for
> us.
>
> The following paper:
> Vanni, S., Neri, M., Tavernelli, I., and Rothlisberger, U.: Predicting
> Novel Binding Modes of
> Agonists to Adrenergic Receptors Using All-Atom Molecular Dynamics
> Simulations. PLoS
> Comput Biol 7, e1001053 (2011)
>
> Uses Amber99SB over 500-800+ns for their beta2-adrenergic receptor system.
>
> On 2012-04-19 12:02:36PM +0530, Anirban Ghosh wrote:
> > Hi ALL,
> >
> > When running a membrane protein (say GPCR) in a lipid bilayer (say POPC
> or
> > DPPC etc.) which according to your experience is the most suited
> > force-field in GROMACS that best retains the 7TM / secondary structures
> of
> > the protein over long simulations? I have tried running with ff53a6 (as
> > suggested in Justin's tutorial), but find that the helices in the bilayer
> > tend to lose their helicity over time and turns into coils. ff43a2 seems
> to
> > do the job somewhat better by retaining the helicity. Will ff43a1 work
> even
> > better as the principle aim is to observe changes in the protein without
> > losing its secondary structures? Your experience please.
> > Thanks a lot in advance.
> >
> >
> > Regards,
> >
> > Anirban
>
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> ==
> Peter C. Lai| University of Alabama-Birmingham
> Programmer/Analyst  | KAUL 752A
> Genetics, Div. of Research  | 705 South 20th Street
> p...@uab.edu | Birmingham AL 35294-4461
> (205) 690-0808  |
> ==
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] Heme group with CHARMM27 FF

[Sundar Jubilant]

Dear gmx-users,

I am new to Gromacs and trying to simulate a protein with a heme group using 
CHARMM27 ff in Gromacs 4.5.3. I have received the following error while running 
pdb2gmx .

WARNING: atom HA is missing in residue HEM 513 in the pdb file
 You might need to add atom HA to the hydrogen database of building 
block HEME
 in the file aminoacids.hdb (see the manual)


WARNING: atom HB is missing in residue HEM 513 in the pdb file
 You might need to add atom HB to the hydrogen database of building 
block HEME
 in the file aminoacids.hdb (see the manual)


WARNING: atom HC is missing in residue HEM 513 in the pdb file
 You might need to add atom HC to the hydrogen database of building 
block HEME
 in the file aminoacids.hdb (see the manual)

.
.
.
.
.
---
Program pdb2gmx, VERSION 4.5.3
Source code file: pdb2top.c, line: 1449

Fatal error:
There were 30 missing atoms in molecule Protein, 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
---

Can anyone help how can I generate and add hydrogen database information for 
heme to be used with CHARMM27 ff?

Thanks,

Sundar Jubilant
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Re: [gmx-users] Heme group with CHARMM27 FF

[Mark Abraham]

On 20/04/2012 2:33 PM, Sundar Jubilant wrote:

Dear gmx-users,

I am new to Gromacs and trying to simulate a protein with a heme group 
using CHARMM27 ff in Gromacs 4.5.3. I have received the following 
error while running pdb2gmx .


When asking for help, please give your full command lines and/or 
interactive selections so that we can know more context.




WARNING: atom HA is missing in residue HEM 513 in the pdb file
 You might need to add atom HA to the hydrogen database of 
building block HEME

 in the file aminoacids.hdb (see the manual)


WARNING: atom HB is missing in residue HEM 513 in the pdb file
 You might need to add atom HB to the hydrogen database of 
building block HEME

 in the file aminoacids.hdb (see the manual)


WARNING: atom HC is missing in residue HEM 513 in the pdb file
 You might need to add atom HC to the hydrogen database of 
building block HEME

 in the file aminoacids.hdb (see the manual)

.
.
.
.
.
---
Program pdb2gmx, VERSION 4.5.3
Source code file: pdb2top.c, line: 1449

Fatal error:
There were 30 missing atoms in molecule Protein, 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
---

Can anyone help how can I generate and add hydrogen database 
information for heme to be used with CHARMM27 ff?


You'll have to read the applicable sections of manual chapter 5, make a 
local copy of the charmm27.ff folder in your working directory and 
editing aminoacids.hdb to add the generation information. When you're 
done, please post your efforts so that others might be able to benefit 
from them in future. (Also, search first in case this has already happened!)


Mark
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Re: [gmx-users] Heme group with CHARMM27 FF

[Sundar Jubilant]

 

 Dear Abraham,

Thanks for your email. I have already read the manual to solve the problem but 
I wasn't successful.

I need little more detailed answer to solve the problem. 

By the way, here is the full command line for which I got the error.

$ pdb2gmx -f CYP.pdb -o CYP_CHARMM.pdb -p CYP1_CHARMM.top -i CYP_CHARMM.itp 
-ignh

The error is

WARNING: atom HA is missing in residue HEM 513 in the pdbfile
 You might need to add atom HA to the hydrogen
database of building block HEME
 in the file aminoacids.hdb (see the manual)


WARNING: atom HB is missing in residue HEM 513 in the pdb   
 file
 You might need to add atom HB to the hydrogen
database of building block HEME
 in the file aminoacids.hdb (see the manual)


WARNING: atom HC is missing in residue HEM 513 in the pdb   
 file
 You might need to add atom HC to the hydrogen
database of building block HEME
 in the file aminoacids.hdb (see the manual)

.
.
.
.
.
---
Program pdb2gmx, VERSION 4.5.3
Source code file: pdb2top.c, line: 1449

Fatal error:
There were 30 missing atoms in molecule Protein, 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
---

Thanks.

Sundar Jubilant


 

-Original Message-
From: Mark Abraham 
To: Discussion list for GROMACS users 
Sent: Fri, Apr 20, 2012 2:17 pm
Subject: Re: [gmx-users] Heme group with CHARMM27 FF


  On 20/04/2012 2:33 PM, Sundar Jubilant wrote:
Dear gmx-users,

I am new to Gromacs and trying to simulate a protein with a 
   heme group using CHARMM27 ff in Gromacs 4.5.3. I havereceived 
the following error while running pdb2gmx .
  

When asking for help, please give your full command lines and/or
interactive selections so that we can know more context.



WARNING: atom HA is missing in residue HEM 513 in the pdb   
 file
 You might need to add atom HA to the hydrogen
database of building block HEME
 in the file aminoacids.hdb (see the manual)


WARNING: atom HB is missing in residue HEM 513 in the pdb   
 file
 You might need to add atom HB to the hydrogen
database of building block HEME
 in the file aminoacids.hdb (see the manual)


WARNING: atom HC is missing in residue HEM 513 in the pdb   
 file
 You might need to add atom HC to the hydrogen
database of building block HEME
 in the file aminoacids.hdb (see the manual)

.
.
.
.
.
---
Program pdb2gmx, VERSION 4.5.3
Source code file: pdb2top.c, line: 1449

Fatal error:
There were 30 missing atoms in molecule Protein, 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
---

Can anyone help how can I generate and add hydrogen database
information for heme to be used with CHARMM27 ff?


  You'll have to read the applicable sections of manual chapter 
 5, make a local copy of the charmm27.ff folder in your working  
directory and editing aminoacids.hdb to add the generation  
information. When you're done, please post your efforts so  that others 
might be able to benefit from them in future.  (Also, search first in 
case this has already happened!)
  
  Mark
  
 
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before posting!
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Re: [gmx-users] Heme group with CHARMM27 FF

[Mark Abraham]

On 20/04/2012 4:38 PM, Sundar Jubilant wrote:


Dear Abraham,

Thanks for your email. I have already read the manual to solve the 
problem but I wasn't successful.


That's good to say (particularly the first time you post a request for 
help, else you'll just get told to go and read), but is unlikely to get 
much help because you haven't identified a specific problem. You'd like 
the ability to build hydrogen atoms on a heme residue. pdb2gmx has to 
have a specific recipe for doing that. The manual describes the required 
format and gives an example. Someone's going to have to do some work.




I need little more detailed answer to solve the problem.

By the way, here is the full command line for which I got the error.

$ pdb2gmx -f CYP.pdb -o CYP_CHARMM.pdb -p CYP1_CHARMM.top -i 
CYP_CHARMM.itp -ignh


If you don't ignore hydrogens, and they're already correct, you don't 
need to re-generate them...


Mark



The error is

WARNING: atom HA is missing in residue HEM 513 in the pdb file
 You might need to add atom HA to the hydrogen database of 
building block HEME

 in the file aminoacids.hdb (see the manual)


WARNING: atom HB is missing in residue HEM 513 in the pdb file
 You might need to add atom HB to the hydrogen database of 
building block HEME

 in the file aminoacids.hdb (see the manual)


WARNING: atom HC is missing in residue HEM 513 in the pdb file
 You might need to add atom HC to the hydrogen database of 
building block HEME

 in the file aminoacids.hdb (see the manual)

.
.
.
.
.
---
Program pdb2gmx, VERSION 4.5.3
Source code file: pdb2top.c, line: 1449

Fatal error:
There were 30 missing atoms in molecule Protein, 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
---

Thanks.

Sundar Jubilant


-Original Message-
From: Mark Abraham 
To: Discussion list for GROMACS users 
Sent: Fri, Apr 20, 2012 2:17 pm
Subject: Re: [gmx-users] Heme group with CHARMM27 FF

On 20/04/2012 2:33 PM, Sundar Jubilant wrote:

Dear gmx-users,

I am new to Gromacs and trying to simulate a protein with a heme 
group using CHARMM27 ff in Gromacs 4.5.3. I have received the 
following error while running pdb2gmx .


When asking for help, please give your full command lines and/or 
interactive selections so that we can know more context.




WARNING: atom HA is missing in residue HEM 513 in the pdb file
 You might need to add atom HA to the hydrogen database of 
building block HEME

 in the file aminoacids.hdb (see the manual)


WARNING: atom HB is missing in residue HEM 513 in the pdb file
 You might need to add atom HB to the hydrogen database of 
building block HEME

 in the file aminoacids.hdb (see the manual)


WARNING: atom HC is missing in residue HEM 513 in the pdb file
 You might need to add atom HC to the hydrogen database of 
building block HEME

 in the file aminoacids.hdb (see the manual)

.
.
.
.
.
---
Program pdb2gmx, VERSION 4.5.3
Source code file: pdb2top.c, line: 1449

Fatal error:
There were 30 missing atoms in molecule Protein, 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
---

Can anyone help how can I generate and add hydrogen database 
information for heme to be used with CHARMM27 ff?


You'll have to read the applicable sections of manual chapter 5, make 
a local copy of the charmm27.ff folder in your working directory and 
editing aminoacids.hdb to add the generation information. When you're 
done, please post your efforts so that others might be able to benefit 
from them in future. (Also, search first in case this has already 
happened!)


Mark
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