On 10/28/17 2:24 PM, Rose wrote:
Hello,
this is topol.top
-------
; Include forcefield parameters
#include "amber03.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
ZnS 3
#include "ZnS.itp"
#include "thr.itp"
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "./amber03.ff/tip3p.itp"
[ system ]
; Name
Protein_ligand
[ molecules ]
; Compound #mols
ZnS 1
THR 1
SOL 561
-----
i get this error
Fatal error:
Atomtype P5 not found
For more information and tips for troubleshooting, please check the GROMACS
---------
thr.itp file
[ moleculetype ]
; molname nrexcl
THR 1
[ atoms ]
;id type resnr residu atom cgnr charge mass
1 P5 1 THR BB 1 0 72
2 Nda 1 THR SC1 2 0 0
3 D 1 THR SC2 3 +0.31 36
4 D 1 THR SC3 4 -0.31 36
[virtual_sites2]
; Site from funct a
2 3 4 1 0.5
[bonds]
; i j funct length force.c.
1 2 1 0.26 9000
[constraints]
; i j funct length
3 4 1 0.28
------------------------------------
i think the problem is thr.itp file and its not usable for amber03
so what should i do?do you think the problem is that?
Yes, that's exactly it. You've got what appears to be some kind of
coarse-grained topology for Thr, which is naturally incompatible with an
atomistic force field.
Either find (in the literature) suitable parameters for this
zwitterionic species, or use a different force field that does (hint:
AMBER is the hardest one in this regard, literally every other force
field lets you create zwitterions in pdb2gmx without a problem).
-Justin
--
==================================================
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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