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

[rama david]

Hi Gromacs Friends,
Thank you mark  for your solution .

Sorry for my incomplete information on topic..

The CR atom type in ligand corresponds to the
cyclohexane atoms in the ligands...
I think I have to change the CR name , but what
should be the  new name????

With Best Wishes,
David




On Sat, Apr 21, 2012 at 6:27 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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
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