On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
yes I removed all the old resulting files and did everything again. So now
there is the topology and coordinate file with only NA and CL and not NA+
or CL-.
I also checked whether the molecules are listed in the same order as in
the .gro file and it is the case. So that is also correct.
What do you mean with:
What does your [molecules] directive specify?
My [molecules] part in the topology file looks like this:
[ molecules ]
; Compound #mols
Protein_chain_A 1
DUM 20088
SOL 13428
NA 29
CL 29
I see no reason this would not work. However, I just noticed from your previous
message:
; Include water topology
#include "amber03.ff/tip3p.itp"
; Include topology for ions
#include "amber03.ff/ions.itp"
#include "amber03.ff/spc.itp"
#include "amber03.ff/dum.itp"
You're using two different water models, so things are getting overridden there.
With AMBER03, you should be using TIP3P, not SPC. The conflicting water
models suggest you've made manual modifications to the topology. Perhaps there
is some error as a result.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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