[gmx-users] protein in dppc

[edmund lee]

Dear all and Justin, I have try with the KALP-15 in DPPC tutorials..it was successfully done until Inflategro step.then I tried with my own protein, I still having the same problems, while i wanna do the energy minimization after inflategro.
3 DPPC removed during inflategro...and i updated the number of molecules of DPPC lipid in topology..

here is how the strong_posre.itp file look like
 [ position_restraints ] ; i funct fcx fcy fcz 1 1 100000 100000 100000 2 1 100000 100000 100000 3 1 100000 100000 100000 4 1 100000 100000 100000 5 1 100000 100000 100000 ..... .... ....3483 1 100000 100000 1000003484 1 100000 100000 1000003485 1 100000 100000 1000003486 1 100000 100000 100000
ONLY protein included in the strong_posre.itp file....(this protein has 3486 atoms..)
then again i updated my topology...

; Include forcefield parameters#include "ffG53a6_lipid.itp"

; Include Position restraint file#ifdef POSRES#include "posre.itp"#endif
; Strong position restraints for InflateGRO#ifdef STRONG_POSRES#include "strong_posre.itp"#endif
; Include DPPC chain topology#include "dppc.itp"
; Include chain topologies#include "topol_A.itp"#include "topol_B.itp"
; Include water topology#include "spc.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 ]; Nameprotein in dppc


[ molecules ]; Compound        #molsProtein_A           1Protein_B           1DPPC               125

 and I also add in the "define" line in the energyminimization.mdp file  here is my em.mdp file   define =-DSTRONG_POSRES integrator = steep nsteps = 200 constraints = none emtol = 1000.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = PME ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes   HOWEVER, I still get this error when I proceed to the grompp step.  Fatal error:Syntax error - File strong_posre.itp, line 3 Last line read: '[ position_restraints ]' Invalid order for directive position_restraints 
as Justin commented, only Protein is selected in strong posre, ( yea..i only selected the protein) Can anyone guide me in this? Yr comments and advices are appreciated.








edmund lee wrote:> > Dear Justin and all..> > > > I have been struggled for the pass few weeks...> > I follow the KALP-15 in DPPC tutorials but I am using my own protein > > instead.> > > > I had successfully reached the step INFLATEGRO where 2 lipid removed > > from the upper layer n 2 lipids removed from the lower layer. Then i > > updated my topology with deducted 4 number of molecule of lipid.> > > > then I generated the strong_porse.itp using the following command:> > > > genrestr -f 1_newbox.gro -o strong_posre.itp -fc 100000 100000 100000> > > > here is how the strong_posre.itp file look like> > [ position_restraints ]> > ; i funct fcx fcy fcz> > 1 1 100000 100000 100000> > 2 1 100000 100000 100000> > 3 1 100000 100000 100000> > 4 1 100000 100000 100000> > 5 1 100000 100000 100000> > .....> > ....> > ....> > ...> > 3483 1 100000 100000 100000> > 3484 1 100000 100000 100000> > 3485 1 100000 100000 100000> > 3486 1 100000 100000 100000> > > > then i updated the topology (as shown below)> > > > ; Include Position restraint file> > #ifdef POSRES> > #include "posre.itp"> > #endif> > > > ; Strong position restraints for InflateGRO> > #ifdef STRONG_POSRES> > #include "strong_posre.itp"> > #endif> > > > ; Include DPPC chain topology> > #include "dppc.itp"> > > > ; Include water topology> > #include "spc.itp"> > > > ; System specifications> > [ system ]> > 128-Lipid DPPC Bilayer > > > > [ molecules ]> > ; molecule name nr.> > DPP 124> > SOL 3655> > > > > > > > > > and I also add in the "define" line in the energyminimization.mdp file> > > > here is my em.mdp file > > > > define =-DSTRONG_POSRES> > integrator = steep> > nsteps = 200> > constraints = none> > emtol = 1000.0> > nstcgsteep = 10 ; do a steep every 10 steps of cg> > emstep = 0.01 ; used with steep> > nstcomm = 1> > coulombtype = PME> > ns_type = grid> > rlist = 1.0> > rcoulomb = 1.0> > rvdw = 1.4> > Tcoupl = no> > Pcoupl = no> > gen_vel = no> > nstxout = 0 ; write coords every # step> > optimize_fft = yes> > > > > > HOWEVER, I get this error when I proceed to the grompp step.> > > > Fatal error:> > Syntax error - File strong_posre.itp, line 3> > Last line read:> > '[ position_restraints ]'> > Invalid order for directive position_restraints> > > > Can anyone guide me in this?> > Yr comments and advices are appreciated.> > > > You have several problems:> > 1. Your [molecules] directive makes no reference to the protein that should be > present.> 2. Your "strong_posre.itp" file looks like it refers to the whole system; it > should have been created from the protein only. You don't want to restrain > everything in the system, anyway, and position restraints cannot be applied to a > multiple molecule types in a single [position_restraints] directive.> > -Justin> > > best regards> > > > edmund> > 





 		 	   		  
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