Liu Shiyong wrote:
Hi, Mark,
I tried your suggestion.
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb
+ editconf -f a6.pdb -o a6.gro -d 20.0
+ make_ndx -f a6.pdb -o a6.ndx
+ grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr
title = b
cpp = /usr/bin/cpp
integrator = cg
dt = 0.002 ; ps !
nsteps = 1
rlist = 0.55
nstlist = 0
vdwtype = Cut-off
rvdw = 0.6
coulombtype = Cut-off
epsilon_r = 2
rcoulomb = 0.6
energy_grps = chAANDB_&_!H* chC_&_!H*
;
; Energy minimizing stuff
;
emtol = 100.0
emstep = 0.01
I got the same error.
-------------------------------------------------------
Program grompp, VERSION 4.0.2
Source code file: grompp.c, line: 150
Fatal error:
atoms 1 and 2 in charge group 1 of molecule type 'Protein_A' are in
different energy groups
-------------------------------------------------------
Now I see it. This error is coming up because the atoms are bonded together.
Atoms 1 and 2 are N and H of the N-terminus, right? Actually, Mark explained
this one some time ago:
http://www.gromacs.org/pipermail/gmx-users/2008-January/031725.html
Also, the cut-off's you've chosen (and using cut-off for electrostatics) are
likely to lead to artifacts. Interestingly, this is the third time in as many
days as I have seen bizarre values of rlist, rcoulomb, and rvdw in conjunction
with Gromos96...
-Justin
"It's Against the Rules" (Pulp Fiction)
On Mon, Feb 2, 2009 at 7:05 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote:
Liu Shiyong wrote:
command:
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb
+ editconf -f a6.gro -o a6.gro -d 20.0
+ make_ndx -f a.pdb -o a6.ndx
+ grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr
I think you still don't need two invocations of pdb2gmx. Your only constraint
is that you want chain IDs preserved for your make_ndx command. The PDB format
carries the system size just like the GRO format. Thus
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb
+ editconf -f a6.pdb -o a6.gro -d 20.0
+ make_ndx -f a6.pdb -o a6.ndx
+ grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr
Simpler still is to define your index groups using information other than the
chain ID - as I think someone suggested days ago. Ranges of atom numbers are
also effective.
-------------------------------------------------------
Program grompp, VERSION 4.0.2
Source code file: grompp.c, line: 150
Fatal error:
atoms 1 and 2 in charge group 1 of molecule type
'Protein_A' are
in different energy groups
-------------------------------------------------------
There is still some sort of disconnect between topology numbering
(which is where charge groups are defined), and the structure you
are using. Can you post the first *few* lines of your .pdb file, [
atoms ] section of the .top, and the relevant index groups?
Not necessarily - the assignment of energy groups in the .mdp file is still a
potential source of problems.
Mark
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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