[gmx-users] trjcat error

[Q. Y. HUAN]

Dear all ,
I did a simulation for 2 ns then i extanded the simulation using tpbconv for 
another 2 ns. After that, I tried to combine the two trajectory files by using 
trjcat by using the following command:

trjcat -f md1.xtc extend1.xtc -o combine.xtc

but it showed a warning that it couldn't read the frame from file.

This is the 1st time i use trjcat, so i am wonder whether the command is 
correct or have some problems with the files.

QIU YI HUAN
DEPARTMENT OF CHEMISTRY,
FACULTY OF SCIENCE,
UNIVERSITY PUTRA MALAYSIA,
MALAYSIA.


  
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[gmx-users] (no subject)

[gportel]

Justin A. Lemkul wrote:
>
>
> [EMAIL PROTECTED] wrote:
>>
>> Hi everyone,
>>
>> I'm having problems running an md simulation (with gmx-4.0.2) using vsites
>> and a time step of 4fs. I did generate the tpr with pdb2gmx. The problem
>> seems to occur when the molecule crosses pbc, since the first sign of the
>> simulation not working fine after ~3ns is
>>
>> "
>> Warning: 1-4 interaction between 6 and 8 at distance 6.122 which is larger
>> than the 1-4 table size 2.400 nm
>> These are ignored for the rest of the simulation
>> This usually means your system is exploding,
>> if not, you should increase table-extension in your mdp file
>> or with user tables increase the table size
>> "
>>
>
> This is a commonly reported problem.  See here:
>
> http://wiki.gromacs.org/index.php/blowing_up
>

Thanks, I was aware of this entry in the wiki.

> Also search the list archives; you will pull up several hundred posts
describing the problems other users have faced and how they overcame
them.
>

> Other things that would be helpful to know if you are still having
problems: What does your system contain?  Did it adequately minimize? 
What kind of equilibration procedure did you perform?

It's dna, ions and water. After I placed the appropriate entries in the
ddb and bonded itp, I was checking whether I could go for 4fs, and I
prepared different runs with different time steps. The set-ups that made
the simulation crash were the ones where the dna had the time/chance to
cross pbc. If this did not occur, the simulation went fine (i.e. did not
explode). Also, in the mean time I run a simulation in NVE with the same
settings and I did no observe the crash after 5ns, despite having jumps
over the pbc in the last few hundreds of ps.

I energy minimized the system with steepest descend, repeated a couple of
times. They went fine after some initial lincs warnings. I admit I did not
equilibrate much, however the crash happens after more than 3ns... let's
consider the first 2ns some sort of tempering.

Although my nstxtcout was set low enough to resolve the frames just before
the crash, I strongly suspect it has to do with crossing the pbc I
will run a couple of simulations with output freq. 1 and double check.


>
> 
>
>> Tcoupl   = v-rescale
>> tc_grps  = system
>> tau_t= 0.1
>> ref_t= 300.00
>
> Maybe you want "Protein Non-Protein" instead of "system" here?  But
that's just general advice, without any knowledge of what's in your
system.
>


Right, although I don't think this is the problem. Just wanted to see if
the sim. would run fine for some ns before production runs. Just occured
to me now, I will also try with the old berendsen, just to double check,
since I did not have any problem in NVE.

> -Justin

Thanks for your time!

Guillem

>
>> Pcoupl   = Berendsen
>> Pcoupltype   = isotropic
>> tau_p= 1.0
>> compressibility  = 4.5e-5
>> ref_p= 1.0
>> constraints  = all-bonds
>> constraint-algorithm = Lincs
>> lincs-order  =  6
>> lincs-iter   = 2
>> lincs-warnangle  = 30
>>
>>
>> I've tried, perhaps naively, using both options for periodic_molecule with
>> the same results.
>>
>> I guess it's hard to tell what did go wrong, but perhaps somebody has an
>> idea.. I thought of submitting a bugzilla, but maybe there are some more
>> tests I could do to pin point the problem before. Any ideas?
>>
>>
>> All the best,
>>
>>
>> Guillem
>>
>> Dr. Guillem Portella
>> MMB - Institute for Research in Biomedicine
>> Parc Cientific de Barcelona
>> http://mmb.pcb.ub.es/~gportella
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ___
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>

-- 
Dr. Guillem Portella
MMB - Institute for Research in Biomedicine
Parc Cientific de Barcelona
http://mmb.pcb.ub.es/~gportella


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Re: [gmx-users] crash in gromacs-4.0.2 using vsites and 2fs t.s.

[gportel]

--- Missatge original 
Assumpte:
De:   [EMAIL PROTECTED]
Data: Tue, Novembre 25, 2008 9:52 am
A:"Discussion list for GROMACS users" 
  [EMAIL PROTECTED]
--


ps, I forgot the Subject in the mail!


Justin A. Lemkul wrote:
>
>
> [EMAIL PROTECTED] wrote:
>>
>> Hi everyone,
>>
>> I'm having problems running an md simulation (with gmx-4.0.2) using vsites
>> and a time step of 4fs. I did generate the tpr with pdb2gmx. The problem
>> seems to occur when the molecule crosses pbc, since the first sign of the
>> simulation not working fine after ~3ns is
>>
>> "
>> Warning: 1-4 interaction between 6 and 8 at distance 6.122 which is larger
>> than the 1-4 table size 2.400 nm
>> These are ignored for the rest of the simulation
>> This usually means your system is exploding,
>> if not, you should increase table-extension in your mdp file
>> or with user tables increase the table size
>> "
>>
>
> This is a commonly reported problem.  See here:
>
> http://wiki.gromacs.org/index.php/blowing_up
>

Thanks, I was aware of this entry in the wiki.

> Also search the list archives; you will pull up several hundred posts
describing the problems other users have faced and how they overcame
them.
>

> Other things that would be helpful to know if you are still having
problems: What does your system contain?  Did it adequately minimize?
What kind of equilibration procedure did you perform?

It's dna, ions and water. After I placed the appropriate entries in the
ddb and bonded itp, I was checking whether I could go for 4fs, and I
prepared different runs with different time steps. The set-ups that made
the simulation crash were the ones where the dna had the time/chance to
cross pbc. If this did not occur, the simulation went fine (i.e. did not
explode). Also, in the mean time I run a simulation in NVE with the same
settings and I did no observe the crash after 5ns, despite having jumps
over the pbc in the last few hundreds of ps.

I energy minimized the system with steepest descend, repeated a couple of
times. They went fine after some initial lincs warnings. I admit I did not
equilibrate much, however the crash happens after more than 3ns... let's
consider the first 2ns some sort of tempering.

Although my nstxtcout was set low enough to resolve the frames just before
the crash, I strongly suspect it has to do with crossing the pbc I
will run a couple of simulations with output freq. 1 and double check.


>
> 
>
>> Tcoupl   = v-rescale
>> tc_grps  = system
>> tau_t= 0.1
>> ref_t= 300.00
>
> Maybe you want "Protein Non-Protein" instead of "system" here?  But
that's just general advice, without any knowledge of what's in your
system.
>


Right, although I don't think this is the problem. Just wanted to see if
the sim. would run fine for some ns before production runs. Just occured
to me now, I will also try with the old berendsen, just to double check,
since I did not have any problem in NVE.

> -Justin

Thanks for your time!

Guillem

>
>> Pcoupl   = Berendsen
>> Pcoupltype   = isotropic
>> tau_p= 1.0
>> compressibility  = 4.5e-5
>> ref_p= 1.0
>> constraints  = all-bonds
>> constraint-algorithm = Lincs
>> lincs-order  =  6
>> lincs-iter   = 2
>> lincs-warnangle  = 30
>>
>>
>> I've tried, perhaps naively, using both options for periodic_molecule with
>> the same results.
>>
>> I guess it's hard to tell what did go wrong, but perhaps somebody has an
>> idea.. I thought of submitting a bugzilla, but maybe there are some more
>> tests I could do to pin point the problem before. Any ideas?
>>
>>
>> All the best,
>>
>>
>> Guillem
>>
>> Dr. Guillem Portella
>> MMB - Institute for Research in Biomedicine
>> Parc Cientific de Barcelona
>> http://mmb.pcb.ub.es/~gportella
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [EMAIL PROTECTED]
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>>
>

-- 
Dr. Guillem Portella
MMB - Institute for Research in Biomedicine
Parc Cientific de Barcelona
http://mmb.pcb.ub.es/~gportella



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[gmx-users] how many pairs are exchanged in replica exchange

[sarbani chattopadhyay]

  
Hi,
   I am new to Replica exchange molecular dynamics. 
I obtained the optimal temperature distribution based on the lowest and 
highest 
tempearture and exchange probability from the REMD caclulator , available 
through the 
gromacs homepage.
There were 17 temperaure values as output. I prepared 17  ".tpr" files based on 
the 
temperatures.
What I want to know is that at each attempted step of replica exchange, how 
many pairs of 
replicas will be exchanged, and how this is decided?

Thanks in advance,
Sarbani
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Re: [gmx-users] trjcat error

[Tsjerk Wassenaar]

Hi QIU YI HUAN,

Was it a warning or did it exit without producing output? Please be
more complete in your postings. Maybe a good idea to include the
output of the program?

In case of an error use gmxcheck first on each of the trajectories. It
seems that one of them is giving an error. Then, if you know which
trajectory is wrong, you can use trjconv to read up to the bad frame,
and write a good trajectory. Obviously, you'll miss what comes after
the bad frame.

Cheers,

Tsjerk

On 11/25/08, Q. Y. HUAN <[EMAIL PROTECTED]> wrote:
> Dear all ,
>  I did a simulation for 2 ns then i extanded the simulation using tpbconv for 
> another 2 ns. After that, I tried to combine the two trajectory files by 
> using trjcat by using the following command:
>
>  trjcat -f md1.xtc extend1.xtc -o combine.xtc
>
>  but it showed a warning that it couldn't read the frame from file.
>
>  This is the 1st time i use trjcat, so i am wonder whether the command is 
> correct or have some problems with the files.
>
>  QIU YI HUAN
>  DEPARTMENT OF CHEMISTRY,
>  FACULTY OF SCIENCE,
>  UNIVERSITY PUTRA MALAYSIA,
>  MALAYSIA.
>
>
>
>  ___
>  gmx-users mailing listgmx-users@gromacs.org
>  http://www.gromacs.org/mailman/listinfo/gmx-users
>  Please search the archive at http://www.gromacs.org/search before posting!
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>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] coarse grain in gromacs

[Xavier Periole]

On Mon, 24 Nov 2008 22:28:36 -0500
 "Justin A. Lemkul" <[EMAIL PROTECTED]> wrote:



BIN ZHANG wrote:

Hi,:
 Is it possible to solvate the system using coarse grained water 
molecule?
 I tried command: genbox -cp cg_protein.pdb -cs cgwat.pdb -o 
cg_protein_water.pdb, but get Segmentation fault.
 Can anyone give me some suggestion or basic procedure to build a 
coarse grained system?


I've used genbox with a simple CG system, no problem.  Does you genbox 
function normally for atomistic systems?

I've done this quite a lot and never got any complain! Have a look at
the box size may be!

Note also that when using the CG you have to specify the vdW radius used
to place the water molecules. A value of 0.197 gives a quite good starting
conformation: no big deformation of the box.

XAvier.


-Justin


 Thanks in advance.
Bin


On Nov 24, 2008, at 1:32 AM, Xavier Periole wrote:


On Sun, 23 Nov 2008 21:48:52 -0800
BIN ZHANG <[EMAIL PROTECTED]> wrote:

Hi, all:
   Has anyone done the coarse graining using MARTINI force field?  
Could you give me any suggestion on how to build a coarse grained  
model from the AA system? I checked the 
website(http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html ) and 
it seems to me they only provide a script for coarse graining  
peptide. My AA system will include protein+lipid+water.
The script indeed provides only transformation from AA to CG for 
proteins.

It should be soon available for any AA system.
In the mean time you can do it with a script of your own, choosing the
atoms from your AA file.

XAvier

   Thanks in advance.
Bin
-
The tree of liberty must be refreshed from time to time with the 
blood  of patriots and tyrants.

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-
XAvier Periole - PhD

- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
-
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-
The tree of liberty must be refreshed from time to time with the blood 
of patriots and tyrants.


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--


Justin A. Lemkul
Graduate Research Assistant
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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-
XAvier Periole - PhD

- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
-
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[gmx-users] trjcat problems

[Q. Y. HUAN]

Dear all,

After trjcat, I wish to view the combined trajactory using ngmx. The problem 
is, how can i get the tpr combined file in oder to view the trajectory using 
ngmx?

thanks for the help

QIU YI HUAN
DEPARTMENT OF CHEMISTRY,
FACULTY OF SCIENCE,
UNIVERSITY PUTRA MALAYSIA,
MALAYSIA.


  
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[gmx-users] Loss of bonds in HEME iron after pdb2gmx

[saradas]

Hello,
I am working with the simulation of cytochromeP450. In the output of the
pdb2gmx command, the iron atom in the HEME loses all the bonds, including
the sulphide bond with cystine. Also, the command changed the residue name
from HEME to HEC. During the execution of the pdb2gmx, I get this warning:

Warning: 'HEC' not found in residue topology database, trying to use 'HEME'

Can someone please tell me, if this is responsible for the loss of bonds
especially the one between CYS and FE. How can the bonds be retained?
Thanks.
Sarada





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[gmx-users] DPPC simulations

[Jenny Hsu]

Hi all

when i run grompp
but it gives "Atomtype LC3 not found"

Could anyone explain me briefly?

Jenny Hsu
--
Jenny Hsu, Biotechnology Dept.,
Ming Chuan University, Taiwan, R.O.C
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[gmx-users] Re: gmx-users Digest, Vol 55, Issue 130

[servaas]

This is the code from repl_ex.c important for your question:
 
In the function get_replica_exchange:

m= (step / re->nst) %2; 
#re->nst=number of steps that you give with the -replex option
  for(i=1; inrepl; i++) {
a = re->ind[i-1];
b = re->ind[i];
bPrint = (re->repl==a || re->repl==b);
if (i % 2 == m) {
check for exchange
}
When step/re->nst is odd m is 1 result is the e.g. for a system with 3
replicas and a swap attempt every 500 steps:
step500   0 x 1   2
step1000  0   1 x 2
step1500  0 x 1   2
etc...

So when step/re-nst is odd exchange is attempted between odd replicas
and odd replica -1, when step/re-nst is even exchange is attempted
between even replica and even replica -1.

hope this helps,

servaas


On Tue, 2008-11-25 at 10:05 +0100, [EMAIL PROTECTED] wrote:
> --
> 
> Message: 5
> Date: 25 Nov 2008 09:05:35 -
> From: "sarbani chattopadhyay" <[EMAIL PROTECTED]>
> Subject: [gmx-users] how many pairs are exchanged in replica exchange
> To: "gmx_users" 
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset="iso-8859-1"
> 
>  
> Hi,
>I am new to Replica exchange molecular dynamics. 
> I obtained the optimal temperature distribution based on the
> lowest and highest 
> tempearture and exchange probability from the REMD caclulator ,
> available through the 
> gromacs homepage.
> There were 17 temperaure values as output. I prepared 17  ".tpr" files
> based on the 
> temperatures.
> What I want to know is that at each attempted step of replica
> exchange, how many pairs of 
> replicas will be exchanged, and how this is decided?
> 
> Thanks in advance,
> Sarbani
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://www.gromacs.org/pipermail/gmx-users/attachments/20081125/1b326dcb/attachment-0001.html
> 
> --

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[gmx-users] location of specbond.dat-solved

[saradas]

Hello,
The file in the local directory is the one that is considered. I am sorry
for the previous mail.
Regards,
Sarada
Graduate student,
NCBS, Bangalore.

Hello,
> I am working in a cluster environment and so, all files there including
> specbond.dat file are write protected. Can someone indicate how I can
> specify that the program must consider the modified file (specbond.dat) in
> my local working directory rather than the one in the main directory?
> Thanks.
> Sarada
>


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[gmx-users] location of specbond.dat

[saradas]

Hello,
I am working in a cluster environment and so, all files there including
specbond.dat file are write protected. Can someone indicate how I can 
specify that the program must consider the modified file (specbond.dat) in
my local working directory rather than the one in the main directory?
Thanks.
Sarada

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[gmx-users] Re:

[Yang Ye]

Hi,

You only need to give ngmx 1) combined xtc files 2) single tpr file in
order to visualize the trajectory.

YY


>
> Dear all,
>
> After trjcat, I wish to view the combined trajactory using ngmx. The problem 
> is, how can i get the tpr combined file in oder to view the trajectory using 
> ngmx?
>
> thanks for the help
>
> QIU YI HUAN
> DEPARTMENT OF CHEMISTRY,
> FACULTY OF SCIENCE,
> UNIVERSITY PUTRA MALAYSIA,
> MALAYSIA.
>
>
>
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-- 
Regards,
Yang Ye
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Re: [gmx-users] trjcat problems

[Justin A. Lemkul]

Q. Y. HUAN wrote:

Dear all,

After trjcat, I wish to view the combined trajactory using ngmx. The problem 
is, how can i get the tpr combined file in oder to view the trajectory using 
ngmx?



No such "combined" .tpr file is necessary; it wouldn't make any sense.  What's 
in a .tpr?  Initial coordinates and simulation parameters - would it make sense 
to concatenate such information?


Use the .tpr file that you used to run the initial MD as input into ngmx.  The 
.tpr is simply used to read in the initial coordinates and allow for the display 
of a subset of atoms (much like all Gromacs tools).


-Justin


thanks for the help

QIU YI HUAN
DEPARTMENT OF CHEMISTRY,
FACULTY OF SCIENCE,
UNIVERSITY PUTRA MALAYSIA,
MALAYSIA.


  
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--


Justin A. Lemkul
Graduate Research Assistant
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] DPPC simulations

[Justin A. Lemkul]

Jenny Hsu wrote:

Hi all
 
when i run grompp

but it gives "Atomtype LC3 not found"
 
Could anyone explain me briefly?
 


There's lots of information about this type of error in the list archives. 
Take, for example:


http://www.gromacs.org/pipermail/gmx-users/2004-August/011867.html

-Justin


Jenny Hsu
--
Jenny Hsu, Biotechnology Dept.,
Ming Chuan University, Taiwan, R.O.C




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Graduate Research Assistant
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] Loss of bonds in HEME iron after pdb2gmx

[saradas]

Hello,
Sorry, I realised the HEME HEC naming was not the problem. But still the
pdb2gmx causes loss of all bonds of FE in HEME. The cystine also gets
protonated and doesnot form a bond with HEME. I tried to preserve the
bonds by editing the specbond.dat file. I do not know if it can be used
for intramolecular bonding. Kindly inform if the modifications I have made
are valid. The runtime information during the execution of pdb2gmx
indicated the linking of FE in HEME to the N atoms. However, I do not see
the bonds when I open the output file in Pymol. Please indicate how this
problem can be resolved.

This is the content of my specbond.dat file:

5
CYS SG  1   HEMEFE  5   0.25CYS HEME
HEMEFE  5   HEMENA  3   0.22HEMEHEME
HEMEFE  5   HEMENB  3   0.22HEMEHEME
HEMEFE  5   HEMENC  3   0.22HEMEHEME
HEMEFE  5   HEMEND  3   0.22HEMEHEME

And these I obtained during the execution of pdbgmx:

Opening library file specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
Special Atom Distance matrix:
  CYS122  CYS135  CYS143  CYS146  CYS150  CYS237  CYS309
   SG958  SG1059  SG1118  SG1136  SG1165  SG1902  SG2475
  CYS135  SG1059   1.677
  CYS143  SG1118   1.076   1.092
  CYS146  SG1136   1.313   1.792   0.749
  CYS150  SG1165   1.175   2.054   0.978   0.426
  CYS237  SG1902   2.194   3.510   2.536   1.933   1.632
  CYS309  SG2475   1.745   2.703   2.469   2.507   2.423   2.449
  CYS343  SG2748   4.679   4.998   4.364   3.763   3.870   3.329   4.426
  CYS406  SG3265   2.258   2.657   2.051   1.603   1.744   1.886   2.198
  CYS457  SG3657   2.232   0.829   1.894   2.582   2.825   4.173   2.898
 HEME462  FE3693   2.257   2.566   1.949   1.489   1.669   1.956   2.343
 HEME462  NA3694   2.456   2.680   2.110   1.663   1.862   2.118   2.486
 HEME462  NB3695   2.199   2.426   1.883   1.498   1.704   2.088   2.247
 HEME462  NC3696   2.061   2.462   1.795   1.321   1.479   1.809   2.217
 HEME462  ND3697   2.331   2.711   2.031   1.505   1.657   1.841   2.455
  CYS343  CYS406  CYS457 HEME462 HEME462 HEME462 HEME462
  SG2748  SG3265  SG3657  FE3693  NA3694  NB3695  NC3696
  CYS406  SG3265   2.501
  CYS457  SG3657   5.547   3.210
 HEME462  FE3693   2.512   0.219   3.147
 HEME462  NA3694   2.361   0.325   3.240   0.211
 HEME462  NB3695   2.647   0.293   2.977   0.208   0.295
 HEME462  NC3696   2.671   0.286   3.064   0.209   0.420   0.297
 HEME462  ND3697   2.389   0.314   3.318   0.208   0.297   0.416   0.293


Linking HEME-462 FE-3693 and HEME-462 NA-3694...
Linking HEME-462 FE-3693 and HEME-462 NB-3695...
Linking HEME-462 FE-3693 and HEME-462 NC-3696...
Linking HEME-462 FE-3693 and HEME-462 ND-3697...
N-terminus: PRO-NH2+
C-terminus: COO-
Now there are 462 residues with 4749 atoms
Making bonds...

Thanks.
Sarada
Graduate Student,
NCBS, Bangalore




Hello,
I am working with the simulation of cytochromeP450. In the output of the
pdb2gmx command, the iron atom in the HEME loses all the bonds, including
the sulphide bond with cystine. Also, the command changed the residue name
from HEME to HEC. During the execution of the pdb2gmx, I get this warning:

Warning: 'HEC' not found in residue topology database, trying to use 'HEME'

Can someone please tell me, if this is responsible for the loss of bonds
especially the one between CYS and FE. How can the bonds be retained?
Thanks.
Sarada






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Re: [gmx-users] DPPC simulations

[Jenny Hsu]

Dear Justin:

I try to include lipid.itp into ffgmxnb.itp
and I also tried to add the different sections [ atomtypes ], [ pairtypes ],
etc... of the lipid.itp files to ffgmx* files
but when i run grompp, i got another fetal error
"Atomtype 'C' not found"

Jenny


2008/11/25 Justin A. Lemkul <[EMAIL PROTECTED]>

>
>
> Jenny Hsu wrote:
>
>> Hi all
>>  when i run grompp
>> but it gives "Atomtype LC3 not found"
>>  Could anyone explain me briefly?
>>
>>
>
> There's lots of information about this type of error in the list archives.
> Take, for example:
>
> http://www.gromacs.org/pipermail/gmx-users/2004-August/011867.html
>
> -Justin
>
>  Jenny Hsu
>> --
>> Jenny Hsu, Biotechnology Dept.,
>> Ming Chuan University, Taiwan, R.O.C
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
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>> interface or send it to [EMAIL PROTECTED]
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>>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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>



-- 
Jenny Hsu, Biotechnology Dept.,
Ming Chuan University, Taiwan, R.O.C
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Re: [gmx-users] Loss of bonds in HEME iron after pdb2gmx

[Justin A. Lemkul]

[EMAIL PROTECTED] wrote:

Hello,
Sorry, I realised the HEME HEC naming was not the problem. But still the
pdb2gmx causes loss of all bonds of FE in HEME. The cystine also gets
protonated and doesnot form a bond with HEME. I tried to preserve the
bonds by editing the specbond.dat file. I do not know if it can be used
for intramolecular bonding. Kindly inform if the modifications I have made
are valid. The runtime information during the execution of pdb2gmx
indicated the linking of FE in HEME to the N atoms. However, I do not see
the bonds when I open the output file in Pymol. Please indicate how this
problem can be resolved.



Well, using visualization software may not indicate anything.  Most programs 
decide on bonds based on distance, not any sort of intelligent mechanism.  The 
question is whether or not these bonds show up in your topol.top.



This is the content of my specbond.dat file:

5
CYS SG  1   HEMEFE  5   0.25CYS HEME


Well, this may be why your Cys is getting protonated - you're telling pdb2gmx 
that it should be!  See the format of specbond.dat here:


http://wiki.gromacs.org/index.php/specbond.dat

The second-to-last column should be the new residue name for cysteine, probably 
you want something like CYS2.



HEMEFE  5   HEMENA  3   0.22HEMEHEME
HEMEFE  5   HEMENB  3   0.22HEMEHEME
HEMEFE  5   HEMENC  3   0.22HEMEHEME
HEMEFE  5   HEMEND  3   0.22HEMEHEME



Why is this section (above) even necessary?  Are these bonds not defined in the 
.rtp file of your force field?  Which force field are you using?  I know these 
are defined in the Gromos-type force fields.


Try again with the original specbond.dat, but don't assume that visualization 
software will always indicate the presence/absence of a bond.  Examine your 
topology for that.


-Justin


And these I obtained during the execution of pdbgmx:

Opening library file specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
Special Atom Distance matrix:
  CYS122  CYS135  CYS143  CYS146  CYS150  CYS237  CYS309
   SG958  SG1059  SG1118  SG1136  SG1165  SG1902  SG2475
  CYS135  SG1059   1.677
  CYS143  SG1118   1.076   1.092
  CYS146  SG1136   1.313   1.792   0.749
  CYS150  SG1165   1.175   2.054   0.978   0.426
  CYS237  SG1902   2.194   3.510   2.536   1.933   1.632
  CYS309  SG2475   1.745   2.703   2.469   2.507   2.423   2.449
  CYS343  SG2748   4.679   4.998   4.364   3.763   3.870   3.329   4.426
  CYS406  SG3265   2.258   2.657   2.051   1.603   1.744   1.886   2.198
  CYS457  SG3657   2.232   0.829   1.894   2.582   2.825   4.173   2.898
 HEME462  FE3693   2.257   2.566   1.949   1.489   1.669   1.956   2.343
 HEME462  NA3694   2.456   2.680   2.110   1.663   1.862   2.118   2.486
 HEME462  NB3695   2.199   2.426   1.883   1.498   1.704   2.088   2.247
 HEME462  NC3696   2.061   2.462   1.795   1.321   1.479   1.809   2.217
 HEME462  ND3697   2.331   2.711   2.031   1.505   1.657   1.841   2.455
  CYS343  CYS406  CYS457 HEME462 HEME462 HEME462 HEME462
  SG2748  SG3265  SG3657  FE3693  NA3694  NB3695  NC3696
  CYS406  SG3265   2.501
  CYS457  SG3657   5.547   3.210
 HEME462  FE3693   2.512   0.219   3.147
 HEME462  NA3694   2.361   0.325   3.240   0.211
 HEME462  NB3695   2.647   0.293   2.977   0.208   0.295
 HEME462  NC3696   2.671   0.286   3.064   0.209   0.420   0.297
 HEME462  ND3697   2.389   0.314   3.318   0.208   0.297   0.416   0.293


Linking HEME-462 FE-3693 and HEME-462 NA-3694...
Linking HEME-462 FE-3693 and HEME-462 NB-3695...
Linking HEME-462 FE-3693 and HEME-462 NC-3696...
Linking HEME-462 FE-3693 and HEME-462 ND-3697...
N-terminus: PRO-NH2+
C-terminus: COO-
Now there are 462 residues with 4749 atoms
Making bonds...

Thanks.
Sarada
Graduate Student,
NCBS, Bangalore




Hello,
I am working with the simulation of cytochromeP450. In the output of the
pdb2gmx command, the iron atom in the HEME loses all the bonds, including
the sulphide bond with cystine. Also, the command changed the residue name
from HEME to HEC. During the execution of the pdb2gmx, I get this warning:

Warning: 'HEC' not found in residue topology database, trying to use 'HEME'

Can someone please tell me, if this is responsible for the loss of bonds
especially the one between CYS and FE. How can the bonds be retained?
Thanks.
Sarada






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--


Justin A. Lemkul
Graduate Research Assist

Re: [gmx-users] DPPC simulations

[Justin A. Lemkul]

Jenny Hsu wrote:

Dear Justin:
 
I try to include lipid.itp into ffgmxnb.itp

and I also tried to add the different sections [ atomtypes ], [ pairtypes ],
etc... of the lipid.itp files to ffgmx* files


All you should have to do is copy all the sections of lipid.itp into 
ffgmxnb.itp, with the exception of the [ dihedraltypes ], which goes in 
ffgmxbon.itp.  I'm not clear what exactly you've done based on your description.


-Justin


but when i run grompp, i got another fetal error
"Atomtype 'C' not found"
 
Jenny
 
 
2008/11/25 Justin A. Lemkul <[EMAIL PROTECTED] >




Jenny Hsu wrote:

Hi all
 when i run grompp
but it gives "Atomtype LC3 not found"
 Could anyone explain me briefly?
 



There's lots of information about this type of error in the list
archives. Take, for example:

http://www.gromacs.org/pipermail/gmx-users/2004-August/011867.html

-Justin

Jenny Hsu
--
Jenny Hsu, Biotechnology Dept.,
Ming Chuan University, Taiwan, R.O.C




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-- 



Justin A. Lemkul
Graduate Research Assistant
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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--
Jenny Hsu, Biotechnology Dept.,
Ming Chuan University, Taiwan, R.O.C


--


Justin A. Lemkul
Graduate Research Assistant
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] Extracting the water molecules in hydration layer

[Suman Chakrabarty]

Dear all,

is there an easy way to extract only the water molecules in the
hydration layer/shell around the protein/polymer chain? I need them
both for visualization of the trajectory and some analysis.

I can do this by writing my own program alright, but I wanted to know
if there is any in-built prescription within gromacs. I am not being
able to find it.


Thanks,
Suman.
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Re: [gmx-users] Extracting the water molecules in hydration layer

[Xavier Periole]

On Tue, 25 Nov 2008 20:39:37 +0530
 "Suman Chakrabarty" <[EMAIL PROTECTED]> wrote:

Dear all,

is there an easy way to extract only the water molecules in the
hydration layer/shell around the protein/polymer chain? I need them
both for visualization of the trajectory and some analysis.

trjorder would order the solvent based on their distance to the
protein. Then you can use an index to generate a trajectory with only
XX water molecules ..


I can do this by writing my own program alright, but I wanted to know
if there is any in-built prescription within gromacs. I am not being
able to find it.


Thanks,
Suman.
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-
XAvier Periole - PhD

- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
-
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[gmx-users] course grain model for DNA

[He, Yang]

Hi all users,

when I am using the gromacs to simulate the course grain model for DNA, it 
seems that the software doesn't recognize my force field file. I have included 
all the bond and non-bond parameters in the bon.itp and nb.itp file.

During my simulation , I found that the base pair for C-G which first are in 
the balance distance always repel from each other so I try to increase the 
value of epsilon to increase the dispersion between this pair but it still did 
not work and the pair still  repelled  from each other after the simulation .

Then I tried like this "   ;  Gb2  Cb2  1  0.000194e10   0.00217e4 " in 
my nb.itp file,  I found that the simulation can still be carried on and the 
simulation result is the same for this base pair.

So ,I got confused about this phenomenon . Can anyone of you give me some 
suggestions?

Thank you in advance.

Yang
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[gmx-users] Re: how to show dodecahedron box in VMD

[xianghong qi]

Dear all:

I am trying to show the dodecahedron box only in vmd since my simulation box
is dodecahedron.  If I include water, I can see the box is dodecahedron. But
I want to get rid off all of water, then my box will not appear there. How
can I keep the dodecahedron box boundaries and solute only? Looks like only
the rectangular box boundaries can be drawn  in VMD.
Does anyone has some suggestions? Appreciate your great help.
Happy Thanksgiving.
-Xianghong Qi

-- 
Some people make the world more special just by being in it.
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[gmx-users] TYR residue in OPLS-AA

[Chris Neale]

I think that it is worth having a central repository that lists modifications 
to forcefield files during development -- especially
changes as opposed to simple additions. It's not always a huge deal, but it would be nice if this information was easily available. 
Revision history might be one place for it, but the wiki would also suffice.


This change to OPLSAA TYR charge groups appears to have been made between gromacs 3.3.1 and 3.3.3. 



Based on:
http://www.gromacs.org/pipermail/gmx-users/2006-December/025075.html

Adam Mazur wrote:

/ Dear All!
/>/ 
/>/ I have noticed an error in TYR residue in OPLS-AA, Gromacs 3.3.1

/>/ Have a look at ffoplsaanr.rtp:
/>/ CG of TYR should be in the same charge group as CB,HB1 and HB2.
/>/ 
/>/ [ TYR ]

/>/  [ atoms ]
/>/  Nopls_238   -0.500 1
/>/  Hopls_2410.300 1
/>/ CAopls_224B   0.140 1
/>/ HAopls_1400.060 1
/>/ CBopls_149   -0.005 2
/>/HB1opls_1400.060 2
/>/HB2opls_1400.060 2
/>/ CGopls_145   -0.115 3 <---
/>/CD1opls_145   -0.115 4
/>/HD1opls_1460.115 4
/>/ 
/>/ 
/>/ Maybe,  it's not of great importance, but it would be nice to have a correct 
/>/ version.
/>/ 
/Thanks for pointing that out. As long as one is using PME there is no 
difference, but when using cut-offs there might be an issue.


--
David.

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Re: [gmx-users] crash in gromacs-4.0.2 using vsites and 2fs t.s.

[gportel]

Hi everyone,

As I wrote yesterday, I'm having problems running stable simulations with
vsites and constraints in all bonds in different time-steps using
gmx-4.0.2. As long as the dna strand does not cross pbc, the simulations
run fine (the longest I did was 5ns). The dna topology was generated with
pdb2gmx, several details on how the simulations were carried out are
listed in the quoted mails below. I also using -dlb auto, just in case it
matters.

I reproduced the crash in two different machines, different starting and
simulations conditions (rectangular or octahedric boxes, Berendsen and
v-rescale, the two options for periodic_molecule). As I reported before,
it happens when pbc are crossed, this time I'm really sure: I resolved the
steps right before the crash time step by time step, plus the distance
separating the 1-4 interactions (the first warning I get before the crash)
is around the length of the corresponding box vector.

In my first round of attempts I did not observe any crash in these systems
in NPE simulations (before I said NVE, but I do have pressure control)
regardless of pbc crossings. I'm running now tests in this ensemble to see
if I can also reproduce the 'non-crashing' behavior. Problem is, at the
moment, that the dna is cooling down and it does not move much from the
box center :-(, so after 4ns it did not cross any box boundary.


Does anybody have a clue of what can be the problem? Or how to debug it in
a more efficient manner? I'm trying to give the information I suspect
could be useful to narrow it down. I can provide more details, data, input
files, etc...

Thanks for your help!

Guillem

Justin A. Lemkul wrote:
> >
> >
> > [EMAIL PROTECTED] wrote:
>> >>
>> >> Hi everyone,
>> >>
>> >> I'm having problems running an md simulation (with gmx-4.0.2) using
vsites
>> >> and a time step of 4fs. I did generate the tpr with pdb2gmx. The
problem
>> >> seems to occur when the molecule crosses pbc, since the first sign
of the
>> >> simulation not working fine after ~3ns is
>> >>
>> >> "
>> >> Warning: 1-4 interaction between 6 and 8 at distance 6.122 which is
larger
>> >> than the 1-4 table size 2.400 nm
>> >> These are ignored for the rest of the simulation
>> >> This usually means your system is exploding,
>> >> if not, you should increase table-extension in your mdp file or with
user tables increase the table size
>> >> "
>> >>
> >
> > This is a commonly reported problem.  See here:
> >
> > http://wiki.gromacs.org/index.php/blowing_up
> >

Thanks, I was aware of this entry in the wiki.

> > Also search the list archives; you will pull up several hundred posts
describing the problems other users have faced and how they overcame them.
> >

> > Other things that would be helpful to know if you are still having
problems: What does your system contain?  Did it adequately minimize? What
kind of equilibration procedure did you perform?

It's dna, ions and water. After I placed the appropriate entries in the
ddb and bonded itp, I was checking whether I could go for 4fs, and I
prepared different runs with different time steps. The set-ups that made
the simulation crash were the ones where the dna had the time/chance to
cross pbc. If this did not occur, the simulation went fine (i.e. did not
explode). Also, in the mean time I run a simulation in NVE with the same
settings and I did no observe the crash after 5ns, despite having jumps
over the pbc in the last few hundreds of ps.

I energy minimized the system with steepest descend, repeated a couple of
times. They went fine after some initial lincs warnings. I admit I did not
equilibrate much, however the crash happens after more than 3ns... let's
consider the first 2ns some sort of tempering.

Although my nstxtcout was set low enough to resolve the frames just before
the crash, I strongly suspect it has to do with crossing the pbc I
will run a couple of simulations with output freq. 1 and double check.


> >
> > 
> >
>> >> Tcoupl   = v-rescale
>> >> tc_grps  = system
>> >> tau_t= 0.1
>> >> ref_t= 300.00
> >
> > Maybe you want "Protein Non-Protein" instead of "system" here?  But
that's just general advice, without any knowledge of what's in your system.
> >


Right, although I don't think this is the problem. Just wanted to see if
the sim. would run fine for some ns before production runs. Just occured
to me now, I will also try with the old berendsen, just to double check,
since I did not have any problem in NVE.

> > -Justin

Thanks for your time!

Guillem

> >
>> >> Pcoupl   = Berendsen
>> >> Pcoupltype   = isotropic
>> >> tau_p= 1.0
>> >> compressibility  = 4.5e-5
>> >> ref_p= 1.0
>> >> constraints  = all-bonds
>> >> constraint-algorithm = Lincs
>> >> lincs-order  =  6
>> >> lincs-iter   = 2
>> >> lincs-warnangle  = 30
>> >>
>> >>
>> >> I've tried

[gmx-users] correct processing of #define statements by grompp in gromacs 4.0.2 requires exactly one space after #define

[Chris Neale]

When two spaces are included the #define KEYWORD is incompletely removed 
from the file.
In case my conclusion about the exact nature of the error is incorrect, 
here is more information.


I have a ffcharmbon.itp file that contains:

[ dihedraltypes ]
#define  improper_NC2_X_X_C_  180.0  83.68000  2

And an .itp file that contains:

[ dihedrals ]
   1 2 5 8 1 improper_NC2_X_X_C_

where grompp -pp returns

[ dihedrals ]
   1 2 5 8 1 _  180.0  83.68000  2

and the floating '_' character causes the error message:

ERROR 1 [file my.itp, line 77]:
 No default Proper Dih. types

I tried to fix this by removing the trailing underscore character from 
my defined string in both files,

but now I get a trailing 'C'

[ dihedrals ]
   1 2 5 8 1 C  180.0  83.68000  2

So it appears that the define statement is simply not being entirely 
removed.


When I then replaced
#define  improper_NC2_X_X_C_  180.0  83.68000  2
by
#define improper_NC2_X_X_C_  180.0  83.68000  2
(only one space between '#define' and 'improper...')
it works correctly.

Note that cpp handled this original define statement properly in gromacs 
3.3.1.


Chris.





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RE: [gmx-users] correct processing of #define statements by grompp in gromacs 4.0.2 requires exactly one space after #define

[Berk Hess]

Hi,

That  is an annoying bug.
I fixed it for 4.0.3.
If you want it fixed now, the diff is below.

Berk


RCS file: /home/gmx/cvs/gmx/src/kernel/gmxcpp.c,v
retrieving revision 1.9
diff -r1.9 gmxcpp.c
121,122c121,122
<   sscanf(define,"%s",name);
<   ptr = define + strlen(name);
---
>   sscanf(define,"%s%n",name,&i);
>   ptr = define + i;


> Date: Tue, 25 Nov 2008 16:32:57 -0500
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] correct processing of #define statements by grompp in 
> gromacs 4.0.2 requires exactly one space after #define
> 
> When two spaces are included the #define KEYWORD is incompletely removed 
> from the file.
> In case my conclusion about the exact nature of the error is incorrect, 
> here is more information.
> 
> I have a ffcharmbon.itp file that contains:
> 
> [ dihedraltypes ]
> #define  improper_NC2_X_X_C_  180.0  83.68000  2
> 
> And an .itp file that contains:
> 
> [ dihedrals ]
> 1 2 5 8 1 improper_NC2_X_X_C_
> 
> where grompp -pp returns
> 
> [ dihedrals ]
> 1 2 5 8 1 _  180.0  83.68000  2
> 
> and the floating '_' character causes the error message:
> 
> ERROR 1 [file my.itp, line 77]:
>   No default Proper Dih. types
> 
> I tried to fix this by removing the trailing underscore character from 
> my defined string in both files,
> but now I get a trailing 'C'
> 
> [ dihedrals ]
> 1 2 5 8 1 C  180.0  83.68000  2
> 
> So it appears that the define statement is simply not being entirely 
> removed.
> 
> When I then replaced
> #define  improper_NC2_X_X_C_  180.0  83.68000  2
> by
> #define improper_NC2_X_X_C_  180.0  83.68000  2
> (only one space between '#define' and 'improper...')
> it works correctly.
> 
> Note that cpp handled this original define statement properly in gromacs 
> 3.3.1.
> 
> Chris.
> 
> 
> 
> 
> 
> ___
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Re: [gmx-users] course grain model for DNA

[Justin A. Lemkul]

He, Yang wrote:

Hi all users,

when I am using the gromacs to simulate the course grain model for DNA, it 
seems that the software doesn't recognize my force field file. I have included 
all the bond and non-bond parameters in the bon.itp and nb.itp file.

During my simulation , I found that the base pair for C-G which first are in 
the balance distance always repel from each other so I try to increase the 
value of epsilon to increase the dispersion between this pair but it still did 
not work and the pair still  repelled  from each other after the simulation .

Then I tried like this "   ;  Gb2  Cb2  1  0.000194e10   0.00217e4 " in 
my nb.itp file,  I found that the simulation can still be carried on and the simulation 
result is the same for this base pair.



Well, that line is commented out (;), so naturally it would have no effect.

-Justin


So ,I got confused about this phenomenon . Can anyone of you give me some 
suggestions?

Thank you in advance.

Yang
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--


Justin A. Lemkul
Graduate Research Assistant
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] course grain model for DNA

[Mrinalini Puranik]

If there is fraying at the edges only, you can impose distance
restraints on some of the hydrogen bonds at the ends. You need to
modify md.mdp to turn on distance restraints and have a new file
called disres.itp that mentions the distances to be restrained.

Hope this helps,
Mrinalini


On Wed, Nov 26, 2008 at 1:06 AM, He, Yang <[EMAIL PROTECTED]> wrote:
> Hi all users,
>
> when I am using the gromacs to simulate the course grain model for DNA, it 
> seems that the software doesn't recognize my force field file. I have 
> included all the bond and non-bond parameters in the bon.itp and nb.itp file.
>
> During my simulation , I found that the base pair for C-G which first are in 
> the balance distance always repel from each other so I try to increase the 
> value of epsilon to increase the dispersion between this pair but it still 
> did not work and the pair still  repelled  from each other after the 
> simulation .
>
> Then I tried like this "   ;  Gb2  Cb2  1  0.000194e10   0.00217e4 " 
> in my nb.itp file,  I found that the simulation can still be carried on and 
> the simulation result is the same for this base pair.
>
> So ,I got confused about this phenomenon . Can anyone of you give me some 
> suggestions?
>
> Thank you in advance.
>
> Yang
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>



-- 
Mrinalini Puranik
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Re: [gmx-users] how many pairs are exchanged in replica exchange

[Mark Abraham]

sarbani chattopadhyay wrote:
 
Hi,

  I am new to Replica exchange molecular dynamics.
I obtained the optimal temperature distribution based on the lowest 
and highest
tempearture and exchange probability from the REMD caclulator , 
available through the

gromacs homepage.
There were 17 temperaure values as output. I prepared 17  ".tpr" files 
based on the

temperatures.
What I want to know is that at each attempted step of replica exchange, 
how many pairs of

replicas will be exchanged, and how this is decided?


Please read the manual section on Replica Exchange.

Mark
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[gmx-users] correct processing of #define statements by grompp in gromacs 4.0.2 requires exactly one space after #define

[chris . neale]

Nice trick with %n on sscanf. I went with the manual replacement but I  
do appreciate learning new things, thanks Berk,

Chris.

###

Hi,

That  is an annoying bug.
I fixed it for 4.0.3.
If you want it fixed now, the diff is below.

Berk


RCS file: /home/gmx/cvs/gmx/src/kernel/gmxcpp.c,v
retrieving revision 1.9
diff -r1.9 gmxcpp.c
121,122c121,122
<   sscanf(define,"%s",name);
<   ptr = define + strlen(name);
---

  sscanf(define,"%s%n",name,&i);
  ptr = define + i;




Date: Tue, 25 Nov 2008 16:32:57 -0500
From: chris.neale at utoronto.ca
To: gmx-users at gromacs.org
Subject: [gmx-users] correct processing of #define statements by  
grompp in gromacs 4.0.2 requires exactly one space after #define


When two spaces are included the #define KEYWORD is incompletely  
removed from the file.
In case my conclusion about the exact nature of the error is  
incorrect, here is more information.


I have a ffcharmbon.itp file that contains:

[ dihedraltypes ]
#define  improper_NC2_X_X_C_  180.0  83.68000  2

And an .itp file that contains:

[ dihedrals ]
1 2 5 8 1 improper_NC2_X_X_C_

where grompp -pp returns

[ dihedrals ]
1 2 5 8 1 _  180.0  83.68000  2

and the floating '_' character causes the error message:

ERROR 1 [file my.itp, line 77]:
  No default Proper Dih. types

I tried to fix this by removing the trailing underscore character  
from my defined string in both files,

but now I get a trailing 'C'

[ dihedrals ]
1 2 5 8 1 C  180.0  83.68000  2

So it appears that the define statement is simply not being entirely removed.

When I then replaced
#define  improper_NC2_X_X_C_  180.0  83.68000  2
by
#define improper_NC2_X_X_C_  180.0  83.68000  2
(only one space between '#define' and 'improper...')
it works correctly.

Note that cpp handled this original define statement properly in  
gromacs 3.3.1.


Chris.






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[gmx-users] Re: Loss of bonds in HEME iron after pdb2gmx

[saradas]

Hi Justin,
Thanks for your reply. I am using the gmx Gromacs Forcefield. As you said
the topology file does contain the bonds and I need not have made the
modificatins to specbond.dat. But using the original specbond.dat does not
prevent the protonation of CYS. I renamed CYS as CYS2 in the input pdb
file and used the following command line
pdb2gmx_mpi -ignh -ff gmx -f 2c9_s50.pdb -o protein_h.pdb -p  
topology.top -water spce
Am I  missing some crucial option here (like -ss for disulphide bonds)?
Thanks once again.
Regards,
Sarada


> Message: 6
> Date: Tue, 25 Nov 2008 07:17:14 -0500
> From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] Loss of bonds in HEME iron after pdb2gmx
> To: Discussion list for GROMACS users 
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> [EMAIL PROTECTED] wrote:
>> Hello,
>> Sorry, I realised the HEME HEC naming was not the problem. But still the
>> pdb2gmx causes loss of all bonds of FE in HEME. The cystine also gets
>> protonated and doesnot form a bond with HEME. I tried to preserve the
>> bonds by editing the specbond.dat file. I do not know if it can be used
>> for intramolecular bonding. Kindly inform if the modifications I have
>> made
>> are valid. The runtime information during the execution of pdb2gmx
>> indicated the linking of FE in HEME to the N atoms. However, I do not
>> see
>> the bonds when I open the output file in Pymol. Please indicate how this
>> problem can be resolved.
>>
>
> Well, using visualization software may not indicate anything.  Most
> programs
> decide on bonds based on distance, not any sort of intelligent mechanism.
> The
> question is whether or not these bonds show up in your topol.top.
>
>> This is the content of my specbond.dat file:
>>
>> 5
>> CYS SG  1   HEMEFE  5   0.25CYS HEME
>
> Well, this may be why your Cys is getting protonated - you're telling
> pdb2gmx
> that it should be!  See the format of specbond.dat here:
>
> http://wiki.gromacs.org/index.php/specbond.dat
>
> The second-to-last column should be the new residue name for cysteine,
> probably
> you want something like CYS2.
>
>> HEMEFE  5   HEMENA  3   0.22HEMEHEME
>> HEMEFE  5   HEMENB  3   0.22HEMEHEME
>> HEMEFE  5   HEMENC  3   0.22HEMEHEME
>> HEMEFE  5   HEMEND  3   0.22HEMEHEME
>>
>
> Why is this section (above) even necessary?  Are these bonds not defined
> in the
> .rtp file of your force field?  Which force field are you using?  I know
> these
> are defined in the Gromos-type force fields.
>
> Try again with the original specbond.dat, but don't assume that
> visualization
> software will always indicate the presence/absence of a bond.  Examine
> your
> topology for that.
>
> -Justin
>
>> And these I obtained during the execution of pdbgmx:
>>
>> Opening library file specbond.dat
>> 5 out of 5 lines of specbond.dat converted succesfully
>> Special Atom Distance matrix:
>>   CYS122  CYS135  CYS143  CYS146  CYS150  CYS237  CYS309
>>SG958  SG1059  SG1118  SG1136  SG1165  SG1902  SG2475
>>   CYS135  SG1059   1.677
>>   CYS143  SG1118   1.076   1.092
>>   CYS146  SG1136   1.313   1.792   0.749
>>   CYS150  SG1165   1.175   2.054   0.978   0.426
>>   CYS237  SG1902   2.194   3.510   2.536   1.933   1.632
>>   CYS309  SG2475   1.745   2.703   2.469   2.507   2.423   2.449
>>   CYS343  SG2748   4.679   4.998   4.364   3.763   3.870   3.329   4.426
>>   CYS406  SG3265   2.258   2.657   2.051   1.603   1.744   1.886   2.198
>>   CYS457  SG3657   2.232   0.829   1.894   2.582   2.825   4.173   2.898
>>  HEME462  FE3693   2.257   2.566   1.949   1.489   1.669   1.956   2.343
>>  HEME462  NA3694   2.456   2.680   2.110   1.663   1.862   2.118   2.486
>>  HEME462  NB3695   2.199   2.426   1.883   1.498   1.704   2.088   2.247
>>  HEME462  NC3696   2.061   2.462   1.795   1.321   1.479   1.809   2.217
>>  HEME462  ND3697   2.331   2.711   2.031   1.505   1.657   1.841   2.455
>>   CYS343  CYS406  CYS457 HEME462 HEME462 HEME462 HEME462
>>   SG2748  SG3265  SG3657  FE3693  NA3694  NB3695  NC3696
>>   CYS406  SG3265   2.501
>>   CYS457  SG3657   5.547   3.210
>>  HEME462  FE3693   2.512   0.219   3.147
>>  HEME462  NA3694   2.361   0.325   3.240   0.211
>>  HEME462  NB3695   2.647   0.293   2.977   0.208   0.295
>>  HEME462  NC3696   2.671   0.286   3.064   0.209   0.420   0.297
>>  HEME462  ND3697   2.389   0.314   3.318   0.208   0.297   0.416   0.293
>>
>>
>> Linking HEME-462 FE-3693 and HEME-462 NA-3694...
>> Linking HEME-462 FE-3693 and HEME-462 NB-3695...
>> Linking HEME-462 FE-3693 and HEME-462 NC-3696...
>> Linking HEME-462 FE-3693 and HEME-462 ND-3697...
>> N-terminus: PRO-NH2+
>> C-terminus: COO-
>> Now there are 462 residues with 4749 atoms
>> Making bonds...
>>
>> Thanks

[gmx-users] Using double precision files with single precision version

[vivek sharma]

Hi All,
I had a few MD runs with double precision in gromacs, Can I use single
precision version of gromacs to play with those files e.g making movie files
and extracting h_bond information.
I am afraid if it will affect my results.

Please suggest

With thanks,
Vivek
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