[gmx-users] restraint numbering in g_disre output

[Bruce Milne]

Hi,

When g_disre reports restraint violations in the *.log file, what do the 
restraint numbers correspond to?


If I have say 5 restraints in index groups 0 1 2 2 3 and g_disre reports 
a violation on restraint 3 is is talking about index group 3 or the 
third restraint in the file - in this case index # 2?


Cheers,

Bruce

--
"Hamewith - the road that's never dreary"

Dr. Bruce F. Milne MRSC
CEQOFFUP
Faculdade de Farmácia
Universidade do Porto
Rua Aníbal Cunha - 164
4050-047
Porto
Portugal

email: [EMAIL PROTECTED]

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Re: [gmx-users] gmx 3.3.2 explodes with libc.so.6

[Bruce Milne]

Dear Li Qiang,


it seems another guy get the same error(cannot pass gmxtest with
rb1/acetonitrilRF) as me. and it sounds like the compatible problem
between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new.

Herein I just suggest and hope others may help to install 3.3.2 on new
ubuntu 7.10 to confirm the problem. 



I have just installed 3.3.2 on my (64-bit) Ubuntu 7.10 machine 
(dual-core Athlon64 4000+, 2GB RAM) and run the serial tests. All the 
single and double precision tests passed with and without assembly loop 
optimizations so I guess it's not simply Ubuntu 7.10 that is to blame 
(unless what you are seeing is a 32-bit distribution-specific problem?).


Cheers,

Bruce

--
"Hamewith - the road that's never dreary"

Dr. Bruce F. Milne
CEQOFFUP
Faculdade de Farmácia
Universidade do Porto
Rua Aníbal Cunha - 164
4050-047
Porto
Portugal

email: [EMAIL PROTECTED]

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[gmx-users] Re: Problems prior to running lipid-protein simulation

[Bruce Milne]

[EMAIL PROTECTED] wrote:

Bruce Milne wrote:
  
> You don't have to run pdb2gmx for the whole system at any point 


Probably true.
> (it's 
> not going to work anyway unless you add the POPC parameters to all the 
> force field files and then add the POPC residue to the  .rtp file so 
> that  pdb2gmx can recognize it).

Not quite true. The contents of the .itp files don't matter to pdb2gmx 
since it writes a .top file that #includes them. So you need to have a 
working POPC entry in an .rtp file for pdb2gmx, and later on, when 
using grompp, you'll need the former contents of the .rtp file to 
correspond to stuff the .itp files. The latter you need even without 
using pdb2gmx, of course.


Good point. I was only considering the case where you want pdb2gmx to 
provide you with a complete .top file that needs no additions and takes 
all its parameters from the same place (as you would get for a protein 
for example).


Anyway, if you have the .itp files then I think it is easier to simply 
add the required #include lines to the protein.top file so that it 
covers all the molecule types in your coordinate file without trying to 
get pdb2gmx to recognize the lipids.


Cheers,

Bruce

--
"Hamewith - the road that's never dreary"

Dr. Bruce F. Milne
CEQOFFUP
Faculdade de Farmácia
Universidade do Porto
Rua Aníbal Cunha - 164
4050-047
Porto
Portugal

email: [EMAIL PROTECTED]

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[gmx-users] Re: Problems prior to running lipid-protein simulation

[Bruce Milne]

Dear Adak,

[EMAIL PROTECTED] wrote:

Dear All;
when I try to run pdb2gmx command for making .top file of POPC+Protein, an 
error appears: Residue 'POPC' not found in residue topology database.
I have copied all necessary .itp files in share folder and also in the path 
where it is run.
  what could be the problem and how to solve it? (I have passed these steps 
long time ago but now I am not able to reproduce the procedure!)
thanks;


Adak Nasiripour.
  
I think the process you might be wanting to perform is to run pdb2gmx 
for your protein only (with suitably adjusted coordinates so that it 
matches your bilayer coordinates) and then add #include lines to the 
resulting topology to add in the POPC part *after* the force field 
#include statement:


#include "ffgmx.itp"
#include "lipids.itp"
#include "popc.itp"

- assuming that these are your .itp file names. Then adjust the [ 
molecules ] section to list the number and type of your components and 
you should have a working .top file.


You don't have to run pdb2gmx for the whole system at any point (it's 
not going to work anyway unless you add the POPC parameters to all the 
force field files and then add the POPC residue to the  .rtp file so 
that  pdb2gmx can recognize it).


Cheers,

Bruce

--
"Hamewith - the road that's never dreary"

Dr. Bruce F. Milne
CEQOFFUP
Faculdade de Farmácia
Universidade do Porto
Rua Aníbal Cunha - 164
4050-047
Porto
Portugal

email: [EMAIL PROTECTED]

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[gmx-users] Re: regarding NA+atom type

[Bruce Milne]

Hi Vijay,

I've CC'd this email to the gmx-users as it's best to keep this on the list.

There doesn't seem to be any attached .mdp file with your email. Maybe 
it got removed by my mail server.


If you are using ffG43a1 (Gromos96) then the sodium name should be NA+ 
with the charge included just as you were using at the start. So, maybe 
grompp is complaining because it doesn't find the atom type in the 
actual coordinate (.gro) file although it is defined in the topology. 
Maybe you changed the .top file but didn't make the matching change in 
the .gro file. You would also have to delete a water molecule in the 
.gro file and then add your sodium in the position of the deleted water 
so that it matches the .top description. You can do this by hand but 
probably the best way is to use the genion program to do it automatically.


Cheers,

Bruce

vijay kumar hinge vijay wrote:

hi sir .
thanku for reply
i have searched  for the file for force field .atp in my 
GROMACS(3.2.0) .but i haven't got any file like that and i had used 
force field 2(4a1,official).even i checked for the  all  the possibles 
of NA(NA+,NA,Na,na).fortunately my gromacs simulation running by 
changing the my pr.mdp file i think dere might be mistake it my pr.mdp 
file plz can u tel wat might be the reason for this error.i compared 
two pr .mdp files (old,new) came to know that some of the parameters 
are not specified stil im unable find clear error couse.

thanking u
bye
vijay kumar
c/o DR.akash ranjan
cdfd
hyderabad
india

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--
"Hamewith - the road that's never dreary"

Dr. Bruce F. Milne
CEQUIMED
Faculdade de Farmácia
Universidade do Porto
Rua Aníbal Cunha - 164
4050-047
Porto
Portugal

email: [EMAIL PROTECTED]

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[gmx-users] Re: error regarding NA+ atom (vijay kumar hinge vijay)

[Bruce Milne]

Hi,

What force field are you using? It may be that the sodium ion is named 
differently e.g. NA instead of NA+. Check in the force field .atp file 
for the correct name and make sure you use that in your .top file. Maybe 
that's all that's wrong.


Cheers,

Bruce



Respected sir/madem,
i am using gromacs - 3.1.4  version on sunsolaris platform.i got error at
position restrain at grompp step ,telling dat  NO SUCH MOLECULE TYPE
NA+(both are in caps).beofre dat the error which i got , ihv done following
steps
1.first i hv excuted pdb2gmx command den i noted down the charge which given
as out put.charge is -1
2.after editconf(-d 0.9),genbox ,energy minimization(grompp,mdrun)  i had
manipulated da  .top file by adding #include 'ions.itp,removed one water
molecloe from SOL and added NA+ 1 at da end of topology file .
den i got error after runing da grompp of position restrain ,and i had
changed pr.mdp file ,in that i was added da SOL,0.1,300 (temp)
thanking u for ur patiency
regards
vijaya kumar hinge
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"Hamewith - the road that's never dreary"

Dr. Bruce F. Milne
CEQUIMED
Faculdade de Farmácia
Universidade do Porto
Rua Aníbal Cunha - 164
4050-047
Porto
Portugal

email: [EMAIL PROTECTED]

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