[gmx-users] About Doubt in Lipid protein Solvation

vidhya sankar scvsankar_agr at yahoo.com
Wed Oct 31 16:45:53 CET 2012

Dear Justin Thank you For your Previous Kind Reply  

                                                                              I am following your Lipid-protein Tutorial  for My system   I  Gave The Following Commands As Quoted in your Tutorial Also I Have Suitably Edited The Topology As in the Tutorial 

Now the Problem in My solvation . 


I  Gave The Following Commands As Quoted in your Tutorial  

./pdb2gmx_d  -f 2KDQ.pdb -o 2KDQ.gro -ignh -ter -water spc
./editconf_d  -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6  -c
./editconf_d -f dppc128.pdb -o dppc128n.gro -center 3 3 3  -box 6 6 6
./grompp_d -f emdppc.mdp -c dppc128n.gro -p topol_dppc.top  -o emdppc.tpr -maxwarn 1
./trjconv_d -s emdppc.tpr -f dppc128n.gro  -o dppc128_whole.gro  -pbc  mol -ur compact
./editconf_d  -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6  -c
cat 2KDQ_newbox.gro dppc128_whole.gro > system.gro
./genrestr_d  -f 2KDQ_newbox.gro -o strong_posre.itp -fc 100000 100000 100000
perl inflategro.pl system.gro 4 DPPC 18 system_inflated.gro 5 area.dat
./grompp_d -f emdppc.mdp -c system_inflated.gro -p 2KDQ.top  -o 2KDQDPPCem.tpr
./mdrun_d  -v -deffnm 2KDQDPPCem
perl inflategro.pl 2KDQDPPCem.gro 0.95  DPPC 0 system_inflated1.gro 5 area1.dat

I Repeated the inflate and EM  Until I have Attained  APL 66 (Experimental value 62) 

At the End of EMinimised .gro   file The Box vectors  Has been Increased form 6 6  6 6 to 
20.57700  20.57700   6.00000 

As result Box Size Also Increase When I 
solvate   By mere Editing the Vanderwalls Radii  to 0.470,  then my 
system  is is solvated By 64495  Water molecules    How to Avoid this Problem  ?   This is too high  Where I have Committed Mistakes I need your Valuable Ideas  and Suggestions 

Thanks In Advance


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