[gmx-users] Re: Alcohol Dehydrogenase MD simulation....Reg

Mark Abraham Mark.Abraham at anu.edu.au
Sun Mar 27 01:10:30 CET 2011

> Kishore wrote:
>> Dear Mark,
>> As you correctly pointed out, I had looked into those improper 
>> dihedral specifications several times before and it seems that they 
>> are properly mentioned in the .itp file. I have been using the 
>> topologies generated by PRODRG server for NADPH as i could not make 
>> it comply with the inbuilt residue template library topologies. In 
>> this topologies generated by PRODRG there is a directive called [ 
>> dihedrals ] and it listed out all the dihedrals with comment lines 
>> showing proper and improper dihedrals, but this seems to differ from 
>> the way the the topologies are defined in the gromacs inbuilt 
>> template library which only lists out the impropers. Does this make 
>> any difference in terms of grompp interpreting them during the 
>> preprocessing? I am herein pasting a section of that dihedrals and a 
>> snapshot of the NADPH molecule with the atom names labelled so that 
>> you can see that the impropers you mentioned in your reply are infact 
>> mentioned in the .itp file I am using.
>> The three improper dihedrals you have mentioned are highlighted 
>> below...please correct me in case if i am getting the meaning 
>> wrong..Sorry for flooding with long posts, but I am in a great need 
>> for some help on this.
>> [ dihedrals ]
>> ; ai  aj  ak  al  fu    c0, c1, m, ...
>>    1   4   3   2   2      0.0  167.4        0.0  167.4   ; imp   NBS  
>> CBQ  H8M  HBS     4   1   5   6   2      0.0  167.4        0.0  
>> 167.4   ; imp   CBQ  NBS  OBT  CAV     6   4   9   7   2      0.0  
>> 167.4        0.0  167.4   ; imp   CAV  CBQ  CBE  CAN

That looks like the correct function form on reasonable atoms - but 
you'd have to check the naming scheme yourself. Do the charges look 
reasonable to your chemical experience? How does a simulation of just 
NADPH in vacuo go? In a small water box?


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