[gmx-users] Where can i find .itp file for aminoacid for amber03

[Justin Lemkul]

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

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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