[gmx-users] Charm forcefield error..Atomtype CR not found ..

[Mark Abraham]

On 21/04/2012 9:27 PM, rama david wrote:
> Hi Gromacs Friends,
>
> I wish to apply charmff 27 to my protein and ligand
> I proceed in following way ..
>
> 1. I separate the protein and ligand by grep command
>      then delete the ligand lne grom pdb file
> 2  I generate the topology of protein in gromacs
>      using the pdb2gmx command
> 3   I generate the ligand topology by swissparam ,
> 4   I protein top , I added the line..
>
>
> ; Include ligand topology
> #include "ligand.itp"
>
> The ligand.itp generated by swissparam contain position restrain file in it
>
> Ligand itp has following line.....
>   1 CR   1  LIG C1      1  0.0000  12.0110
>     2 CR   1  LIG C2      2  0.0000  12.0110
>     3 CR   1  LIG C3      3  0.0000  12.0110
>     4 CR   1  LIG C4      4  0.0000  12.0110
>     5 CR   1  LIG C5      5  0.0000  12.0110
>     6 CR   1  LIG C6      6  0.0000  12.0110
>     7 CR   1  LIG CM      7  0.5030  12.0110
>     8 NRP  1  LIG N       8 -0.8530  14.0067
>     9 HNRP 1  LIG HN1     9  0.4500   1.0079
>    10 HNRP 1  LIG HN2    10  0.4500   1.0079
>    11 HNRP 1  LIG HN3    11  0.4500   1.0079
>    12 HCMM 1  LIG H1     12  0.0000   1.0079
>    13 HCMM 1  LIG H22    13  0.0000   1.0079
>    14 HCMM 1  LIG H23    14  0.0000   1.0079
>    15 HCMM 1  LIG H32    15  0.0000   1.0079
>    16 HCMM 1  LIG H33    16  0.0000   1.0079
>    17 HCMM 1  LIG H42    17  0.0000   1.0079
>    18 HCMM 1  LIG H43    18  0.0000   1.0079
>    19 HCMM 1  LIG H52    19  0.0000   1.0079
>    20 HCMM 1  LIG H53    20  0.0000   1.0079
>    21 HCMM 1  LIG H62    21  0.0000   1.0079
>    22 HCMM 1  LIG H63    22  0.0000   1.0079
>    23 HCMM 1  LIG HM2    23  0.0000   1.0079
>    24 HCMM 1  LIG HM3    24  0.0000   1.0079
> .
> .
> .
>
> Now when I give the grompp command  I stuck with following error ...
>
>
> Program grompp, VERSION 4.5.4
> Source code file: /build/buildd/gromacs-4.5.4/src/kernel/toppush.c, line: 1166
> Fatal error:
> Atomtype CR not found

The atomtype CR used in ligand .itp corresponds to no [atomtype] entry 
in the standard force field, so grompp is stuck. You need to find out 
why SwissParam thinks this is a reasonable atom type to use, and adapt 
your solution accordingly.

Mark