[gmx-users] multichain peptide simulation

[Susan Idiula]

Hi,

I tried using an index file. it does not seem to work. is there any other
alternative?

thanks
susan


> On Wed, 2004-05-05 at 12:18, Susan Idiula wrote:
>> Hi,
>>
>> I am simulating six heptapeptides (as different chains) in water. Each
>> peptide has the N terminus as -CO-CH3 and the C-terminus as NH-CH3.The
>> simulation works well but when I use xrama and g_rama to check dihedral
>> angles. I get the following error:
>>
>> Fatal error: Dihedral X, Y not found in topology. (X,Y are the atom
>> numbers of O of -CO of 7th residue and Y is the atom number of H of NAC
>> as
>> mentioned in the .top file created by pdb2gmx)
>
> it seems like g_rama is misinterpreting the protein as being a single
> chain. maybe you can use an index file.
>
>>
>> Everything works nicely with one heptapeptide.
>>
>> These are the topology of the extra groups that I have introduced in the
>> ffG43a1.rtp.
>>
>> [ ACE ]
>>  [ atoms ]
>>     CA   CH3   0.000     0
>>      C     C   0.380     1
>>      O     O  -0.380     1
>>  [ bonds ]
>>      C    CA   gb_26
>>      C     O   gb_4
>>      C    +N   gb_9
>>  [ angles ]
>>    CA     C    +N    ga_18
>>     O     C    +N    ga_32
>>    CA     C     O    ga_29
>>  [ impropers ]
>>     C    CA    +N     O    gi_1
>>  [ dihedrals ]
>>    CA  C  +N  +CA  gd_4
>>
>> [ NAC ]
>>  [ atoms ]
>>     N   N   -0.280  0
>>     H   H    0.280  0
>>     CA  CH3  0.000  1
>>  [ bonds ]
>>     N   H    gb_2
>>     N   CA   gb_20
>>  [ angles ]
>>    -C   N   H   ga_31
>>     H   N   CA  ga_17
>>    -C   N   CA  ga_21
>>  [ impropers ]
>>     N  -C   CA   H   gi_1
>>  [ dihedrals ]
>>     -CA -C  N  CA  gd_4
>>
>> I have 7 residues per%2