[gmx-users] [Fwd: How simulate two peptides in a box?]

[David van der Spoel]

gurpreet singh wrote:
> Thanks Mark for your advice
> 
>  I tried to run the simulation even by removing all the restraints as 
> you told but the same problem was coming.
> In your  second reply you asked me to check the topology file. I have a 
> doubt in that, actually what are the things i should look at in the 
> topology file. I have seen my topology file and the related .itp files 
> also but i did not find anything unusual in that.


try
grompp -maxwarn 0

> 
> Following are the contents of my Topology file:
> 
> ; Include forcefield parameters
> #include "ffG43a1.itp"
> 
> ; Include chain topologies
> #include "aquapomut_grom_A.itp"
> #include "aquapomut_grom_B.itp"
> 
> ; Include water topology
> #include "spce.itp"
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
> 
> ; Include generic topology for ions
> #include "ions.itp"
> 
> [ system ]
> ; Name
> Protein in water
> 
> [ molecules ]
> ; Compound        #mols
> Protein_A           1
> Protein_B           1
> SOL                71
> CL-                 6
> SOL             14825
> ~
> 
> As i told to last time that my protein is a dimer. so my question is 
> this problem is becasue of some missing parameter required for  
> realizing  gromacs that its a dimeric protein?
> 
> with regards
> Gurpreet
> 
> On 7/3/07, *Mark Abraham* <mark.abraham at anu.edu.au 
> <mailto:mark.abraham at anu.edu.au>> wrote:
> 
>      >  Hello Gromacs users:
> 
>     Please don't reply to another user's question with a change of topic and
>     not change the subject line of your email. Not doing this means the
>     people
>     who might know the answer for you have no idea in advance what you're
>     going to be asking, and might not bother reading. Best is to start
>     with a
>     new email, not a reply, and to use your subject line sensibly.
> 
>      > I am running a  dimeric protein simulation on Gromacs 3.3 using
>     the force
>      > filed G43a1.
>      >
>      >
>      > For initially minimizing the hydrogen i did some small
>     minimization and
>      > equilibration in the vacuum by maintaining the restraints
>      > then i added ions and water but in the very first minimization i
>     m getting
>      > the following error
> 
>     If you want to keep your credibility, when people have already made a
>     suggestion about how to solve your problem, such as I did here
>     http://www.gromacs.org/pipermail/gmx-users/2007-June/028301.html,
>     when you
>     post the same problem, you should say what happened when you tried their
>     suggestion. They didn't suggest it for their own entertainment.
> 
>     Look at the minimization "trajectory" and see where things are breaking.
>     Have a look at your topology there, read chapter five thoroughly.
> 
>     Mark
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se