[gmx-users] where can i find .itp file for amino acids?

rose rahmani rose.rhmn93 at gmail.com
Sat Oct 28 14:54:19 CEST 2017


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


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