[gmx-users] 1-4 interaction at distance larger than 1

[Yi Hou]

Thank you very much, yes normally, the header of pdb file has remark 465 and
470. I just used the modeller loop to add the missing residues according to
remark 470, and did not add following remark 465, is it right?  because
there are only RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER,
it does not have atoms. By the way, there is a limit for modeller loop, if I
want to addd more resiudes, are there any others softwares which are
recommended.
Thank you very much
Yi 



On 03/08/2009 17:12, "Justin A. Lemkul" <jalemkul at vt.edu> wrote:

> 
> 
> Yi Hou wrote:
>> Dear Justin 
>> Thank you very much
>> My commands are:
>> 1. add hydrogens, get top and gro files
>> pdb2gmx -f 1z92.pdb -o 1z92.gro -p 1z92.top
>> 
> 
> If I'm not mistaken, 1z92 has substantial stretches of missing residues, and
> you 
> probably had to model them in.  I'd look at those regions as being potentially
> problematic.
> 
>> 2. specify the box size, and add water to the system
>> editconf -f 1z92.gro -bt cubic -d 0.7 -o box.gro
>> genbox -cp box.gro -cs spc216.gro -p 1z92.top -o sol.gro
>> 
>> 3. grommpp -f em.mdp -p 1z92.top -c sol.gro -o em.tpr then found the system
>> is charge -3
>> 
>> 4. add 3NA+ ions in the SOL system
>> genion -s em.tpr -p 1z92.tpr -p 1z92.top -o sol_ion.gro -pname NA+ -np 3
>> -nname CL- -nn 0 -random
>> 
>> 5. perform the energy minimization simulation
>> grompp -f em.mdp -p 1z92.top -o sol_ion.gro -o em.tpr
>> mdrun -deffnm em -v
>> 
>> Those commands until now then I should do position constraints and equil
>> simulations with my pr.mdp and md.mdp parameters.
>> I will check my .log file again to see if any errors occur
> 
> I'd stop and diagnose why the minimization failed.  If you can't finish EM,
> there is no point in running any sort of dynamics, equilibration or otherwise.
> 
> -Justin
> 
>> Thank you very much
>> Yi
>> 
>> 
>> On 03/08/2009 15:56, "Justin A. Lemkul" <jalemkul at vt.edu> wrote:
>> 
>>> 
>>> houyi wrote:
>>>> Dear all,
>>>> I guess others have the same problem for me as well, and it may repeat
>>>> to ask it again due to i am new for gromacs- 3.3.3. my protein is
>>>> 1z92.pdb. when i perform the energy minimization , i got this error. but
>>>> when i used for another small protein, which is 1ycr.pdb, it worked well
>>>> for all. i choose the OPLS-AA/L all-atom force field
>>>> my em.mdp is
>>>> title               =  protein
>>>> cpp                 =  /usr/bin/cpp
>>>> define              =  -DFLEX_SPC
>>>> constraints         =  none
>>>> integrator          =  steep
>>>> dt                  =  0.002    ; ps !
>>>> nsteps              =  100
>>>> nstlist             =  10
>>>> ns_type             =  grid
>>>> rlist               =  1.0
>>>> rcoulomb            =  1.0
>>>> rvdw                = 1.0
>>>> ;
>>>> ;       Energy minimizing stuff
>>>> ;
>>>> emtol               =  1000.0
>>>> emstep              =  0.01
>>>> 
>>>> i found the website and some one said change the table extension to 2 or
>>>> 3 or maybe more, it works for this step, but after performing the
>>>> postion constrains, it got the wrong results. so i guess i will not
>>>> change the table extension, and i do not why it only work for small
>>>> protein not for larger one, and i repeated sevel times, such as changing
>>>> timesteps and rlist and rcoulomb and rvdw to 0.9. still not working.
>>>> could anyone help me to explain this.
>>> Your system is blowing up due to some non-physical interaction.  Tweaking
>>> the
>>> table-extension is probably not going to help.  Some general references:
>>> 
>>> http://oldwiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-o
>>> ff
>>> 
>>> http://oldwiki.gromacs.org/index.php/blowing_up
>>> 
>>> Without knowing more about how you prepared the system (exact commands),
>>> then
>>> you will not likely get much more useful advice.  Take a look at where
>>> things
>>> are falling apart (atom numbers printed in the .log file) and see if you can
>>> deduce the source of the problem.
>>> 
>>> -Justin
>>> 
>>>> thank you very much
>>>> Reards,
>>>> Yi
>>>> 
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