[gmx-users] energy groups

[Liu Shiyong]

Hi, Mark,

I tried your suggestion.

+ pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb
+ editconf -f a6.pdb -o a6.gro -d 20.0
+ make_ndx -f a6.pdb -o a6.ndx
+ grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr

title               =  b
cpp                 =  /usr/bin/cpp
integrator          =  cg
dt                  =  0.002    ; ps !
nsteps              =  1
rlist               =  0.55
nstlist             =  0
vdwtype             =  Cut-off
rvdw                =  0.6
coulombtype         =  Cut-off
epsilon_r           =  2
rcoulomb            =  0.6
energy_grps         =  chAANDB_&_!H* chC_&_!H*
;
;       Energy minimizing stuff
;
emtol               =  100.0
emstep              =  0.01

I got the same error.

-------------------------------------------------------
Program grompp, VERSION 4.0.2
Source code file: grompp.c, line: 150

Fatal error:
atoms 1 and 2 in charge group 1 of molecule type 'Protein_A' are in
different energy groups
-------------------------------------------------------

"It's Against the Rules" (Pulp Fiction)




On Mon, Feb 2, 2009 at 7:05 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>
> Liu Shiyong wrote:
>>
>> command:
>>
>> + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro
>> + pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb
>> + editconf -f a6.gro -o a6.gro -d 20.0
>> + make_ndx -f a.pdb -o a6.ndx
>> + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr
>
>
> I think you still don't need two invocations of pdb2gmx. Your only constraint is that you want chain IDs preserved for your make_ndx command. The PDB format carries the system size just like the GRO format. Thus
>
> + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb
> + editconf -f a6.pdb -o a6.gro -d 20.0
> + make_ndx -f a6.pdb -o a6.ndx
>
> + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr
>
> Simpler still is to define your index groups using information other than the chain ID - as I think someone suggested days ago. Ranges of atom numbers are also effective.
>
>
>>        -------------------------------------------------------
>>                      Program grompp, VERSION 4.0.2
>>                      Source code file: grompp.c, line: 150
>>                      Fatal error:
>>                      atoms 1 and 2 in charge group 1 of molecule type
>>               'Protein_A' are
>>                      in different energy groups
>>                            -------------------------------------------------------
>>
>>
>>    There is still some sort of disconnect between topology numbering
>>    (which is where charge groups are defined), and the structure you
>>    are using.  Can you post the first *few* lines of your .pdb file, [
>>    atoms ] section of the .top, and the relevant index groups?
>
>
> Not necessarily - the assignment of energy groups in the .mdp file is still a potential source of problems.
>
> Mark
>
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-- 
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab:    http://vakser.bioinformatics.ku.edu/people
Phone:      (785) 864-1962