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

[Vytautas Rakeviius]

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

[rose rahmani]

Hello,

this is topol.top

---

; Include forcefield parameters
#include "amber03.ff/forcefield.itp"

[ moleculetype ]
; Namenrexcl
 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
THR1

[ atoms ]
;id type resnr residu atom cgnr   chargemass
1   P5 1 THR BB 1  072
2   Nda1 THR SC12  00
3   D  1 THR SC23  +0.3136
4   D  1 THR SC34  -0.3136

[virtual_sites2]
; Site from   funct a
   2 34   1 0.5

[bonds]
;  i j   funct   length  force.c.
   1 21   0.26 9000

[constraints]
;  i j   funct   length
   3 41   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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