qing yang wrote:
Dear gmx-users,
I am try to simulate the protein-drug, and have used drg.itp from prodrg
server2,5(beta). I have also got pro.top from pdb2gmx programs. But when
PRODRG topologies are often unsatisfactory with respect to charges and charge
groups assigned. Looking at the two relevant atom entries you've posted below,
this is almost certainly the case. Please see the following:
http://www.gromacs.org/Documentation/How-tos/Parameterization
None of that is related specifically to your error, but I figured I should tell
you before you waste your time simulating potentially unreliable parameters.
I issue a grompp command for minimization,grompp gives a fatal error.
The error is:
Error 0 [file "unk.itp",line 4]
Not enough parameters
So you've pasted some of your topology below, but what exactly is on line 4?
…..
Fatal error:
Bonded/nonbonded atom type '1' not found!
Is this a separate error? Please post all relevant output, otherwise it gets
confusing.
My pro.top file:
This can't be right. You said pro.top came from pdb2gmx, so there should be
substantially more in it. This is not to say that you need to post the entirety
of your topology, but I doubt what you've shown is correct. This makes it hard
to know if you've placed your #include statements appropriately, etc.
#include “ffg43a1.itp”
#include “unk.itp”
[molecules]
Protein 1
UNK 1
SOL 109324
My drg.itp file:
This snapshot does not provide any really useful information. Which of these
lines, if any, is line 4, where grompp starts complaining? Shouldn't there be a
[moleculetype] directive at the top of your .itp file, at the very least?
Providing accurate information will get you to a solution a lot faster :)
-Justin
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CR1 1 UNK CBF 1 0.003 12.0110
2 HC 1 UNK HBF 1 0.035 1.0080
...............
[ bonds ]
; ai aj fu c0, c1, ...
1 2 2 0.109 12300000.0 0.109 12300000.0 ; CBF HBF
1 3 2 0.139 10800000.0 0.139 10800000.0 ; CBF CBG
.............
[ pairs ]
; ai aj fu c0, c1, ...
1 6 1 ; CBF NBK
1 9 1 ; CBF CBI
.................
[ angles ]
; ai aj ak fu c0, c1, ...
2 1 3 2 120.0 505.0 120.0 505.0 ;
HBF CBF CBG
2 1 13 2 120.0 505.0 120.0 505.0 ;
HBF CBF CBE
................
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
1 13 3 2 2 0.0 167.4 0.0 167.4 ; imp
CBF CBE CBG HBF
3 1 5 4 2 0.0 167.4 0.0 167.4 ; imp
CBG CBF CBH HBG
Maybe someone knows what the problem might be?How can I deal with this
problem?
Thanks for your help!
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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