On 30/12/2017 06:23, Amir Zeb wrote:
Alright Dr. Justin,
Is it kindly possible to get CHARMM-compatible parameters for Mn2+ which
you haven't included in the port?
I'm searching the literature too to find something worthy.
Try to start with following papers:
http://pubs.acs.org/doi/abs/10.1021/jp054177x
http://pubs.acs.org/doi/abs/10.1021/ct400055v
http://www.sciencedirect.com/science/article/pii/S0010854517300383
-Alexandr
Thanks!
~Amir
On Fri, Dec 29, 2017 at 8:17 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 12/29/17 10:39 AM, Amir Zeb wrote:
Thanks Dr. Justin.
I didn't add this stuff by my own.
I have created Mn+2 topology by simple pdb2gmx command.
Someone hacked your files and added it at some point. None of the releases
of the C36 port that I have ever made had contained Mn2+ parameters. There
are CHARMM-compatible parameters that could be added as part of a larger
metal parameter set, but they've never been included in the port.
Regardless, that's what you need to do - add the correct sigma and epsilon
values to ffnonbonded.itp for the MN atom type.
-Justin
~Amir
On Dec 30, 2017 12:21 AM, "Justin Lemkul" <jalem...@vt.edu> wrote:
On 12/29/17 10:11 AM, Amir Zeb wrote:
Hello dear gromacs users,
I want to simulate a protein which has two Mn+2 ions as co-factor.
Till the solvation, I could prepare the system, but at neutralization
step,
grompp gives me this fatal error.
Fatal error:
Atomtype MN not found
My system has this topology for Mn+2:
[ moleculetype ]
; Name nrexcl
Other_chain_C2 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB
chargeB massB
; residue 501 MN2 rtp MN q +2.0
1 MN 501 MN2 MN 1 2 54.94
;
qtot 2
; residue 502 MN2 rtp MN q +2.0
2 MN 502 MN2 MN 2 2 54.94
;
qtot 4
And the Mn+2 has this configuration:
501MN2 MN 4551 5.405 5.564 2.987
502MN2 MN 4552 5.582 5.590 3.497
I have used Charmm36 ff, and the gromacs version is 5.0.6
Please let me know how can I fix this issue?
This is not a standard CHARMM atom type - did you add it yourself? If
so,
what was the source of the parameters? It looks like you have a residue
defined in the .rtp, hence pdb2gmx wrote the topology, but you don't
actually have parameters assigned for the atom type in ffnonbonded.itp.
-Justin
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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