<br><br><div class="gmail_quote">On Fri, May 11, 2012 at 2:18 PM, Sangita Kachhap <span dir="ltr"><<a href="mailto:sangita@imtech.res.in" target="_blank">sangita@imtech.res.in</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Hello all<br>
I am runing Gromacs Tutorial KALP-15 in DPPC (I am using POPC)<br>
I am geeting error during addiotion of ions<br>
Fatal error:<br>
Your solvent group size (12548) is not a multiple of 3<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>
<br>
I have done following:<br>
<br>
GROMACS COMMAND<br>
<br>
1) Generate topol.top using GROMOS96 53A6 parameter set<br>
pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc<br>
<br>
ay prompt select 13, 2, 2<br>
<br>
2) Download:<br>
* dppc128.pdb - the structure of a 128-lipid DPPC bilayer<br>
* dppc.itp - the moleculetype definition for DPPC<br>
* lipid.itp - Berger lipid parameters<br>
<br>
from <a href="http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies" target="_blank">http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies</a><br>
<br>
3) Modify topol.top with:<br>
#include "gromos53a6.ff/forcefield.itp"<br>
<br>
to:<br>
<br>
#include "gromos53a6_lipid.ff/forcefield.itp"<br>
<br>
<br>
&<br>
<br>
; Include Position restraint file<br>
#ifdef POSRES<br>
#include "posre.itp"<br>
#endif<br>
<br>
; Include POPC chain topology<br>
#include "popc.itp"<br>
<br>
; Include water topology<br>
#include "gromos53a6_lipid.ff/spc.itp"<br>
<br>
<br>
<br>
4) cp files<br>
aminoacids.rtp<br>
aminoacids.hdb<br>
aminoacids.c.tdb<br>
aminoacids.n.tdb<br>
aminoacids.r2b<br>
aminoacids.vsd<br>
ff_dum.itp<br>
ffnonbonded.itp<br>
ffbonded.itp<br>
forcefield.itp<br>
ions.itp<br>
spc.itp<br>
watermodels.dat<br>
<br>
from gromacs top to directory named gromos53a6_lipid.ff in working directory.<br>
Append parameter ([ atomtypes ], [ nonbond_params ], and [ pairtypes ])from<br>
lipid.itp to ffnonbonded.itp & ffbonded.itp and create a forcefield.doc file<br>
that contains a description of the force field parameters contain "GROMOS96 53A6<br>
force field, extended to include Berger lipid parameters".<br>
Delete line ";; parameters for lipid-GROMOS interactions." and its subsequent<br>
line, change HW as H of [ nonbond_params ]<br>
<br>
<br>
5) Generate .tpr for POPC<br>
grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr -maxwarn 1<br>
(change OW1, HW2, HW3 to OW, HW and HW2 respectively)<br>
<br>
<br>
6) Remove periodicity<br>
trjconv -s em.tpr -f popc128a.pdb -o popc128a_whole.gro -pbc mol -ur compact<br>
(at command prompt select 0)<br>
<br>
<br>
7) Oriant the KALP peptide within the same coordinate as written in end of<br>
popc128a_whole.gro<br>
editconf -f KALP-15_processed.gro -o KALP_newbox.gro -c -box 6.23910 6.17970<br>
6.91950<br>
<br>
<br>
8) Pack lipid around protein<br>
cat KALP_newbox.gro popc128a_whole.gro > system.gro<br>
Remove unnecessary lines (the box vectors from the KALP structure, the header<br>
information from the DPPC structure) and update the second line of the<br>
coordinate file (total number of atoms) accordingly.<br>
<br>
<br>
9) Modify topol.top to add positional restrain on protein<br>
<br>
; Include Position restraint file<br>
#ifdef POSRES<br>
#include "posre.itp"<br>
#endif<br>
<br>
; Strong position restraints for InflateGRO<br>
#ifdef STRONG_POSRES<br>
#include "strong_posre.itp"<br>
#endif<br>
<br>
; Include DPPC chain topology<br>
#include "dppc.itp"<br>
<br>
; Include water topology<br>
#include "gromos53a6_lipid.ff/spc.itp"<br>
<br>
&<br>
<br>
Genrate new positional restraint<br>
genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 100000 100000 100000<br>
(at prompt select 2)<br>
<br>
Add a line "define = -DSTRONG_POSRES" to .mdp file<br>
<br>
<br>
<br>
<br>
10) Scale down lipid<br>
perl <a href="http://inflategro.pl" target="_blank">inflategro.pl</a> system.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat<br>
system_shrink1.gro<br>
<br>
<br>
11) addion POPC 128 to topol.top<br>
<br>
<br>
12) Solvate with water<br>
Copy vdwradii.dat from Gromacs top to working directory and change the value of<br>
C from 0.15 to 0.375(to avoid addition of water in lipid hydrohphobic core)<br>
<br>
genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro -p<br>
topol.top<br>
<br>
<br>
grompp -f ions.mdp -c system_shrink1_solv.gro -p topol.top -o ions.tpr<br>
<br>
genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname CL -nn 4<br>
(at command prompt select 0)<br></blockquote><div><br></div><div>Is group 0 your solvent? You should chose a group corresponding to the solvent of your system.</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
<br>
So can anyone please help me correct this error.<br>
<br>
<br>
<br>
With regards<br>
Sangita Kachhap<br>
SRF<br>
BIC,IMTECH<br>
CHANDIGARH<br>
<br>
______________________________________________________________________<br>
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)<br>
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