Maybe just rename your custom thr.itp THR and in other places to something else
to avoid conflict with default version?amber03.ff is in
gromacs-version/share/top folder. There you can find aminoacids files with
default amber03 THR.
On Saturday, October 28, 2017, 3:54:41 PM GMT+3, rose rahmani
<rose.rhm...@gmail.com> 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
LYSOZYME in water
[ 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?
i really appreciate you if you help me
with regards
rose
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
