[gmx-users] ACE patch in FFG43a1

[David van der Spoel]

priyanka srivastava wrote:
> 
> Dear All,
> 
> I have a problem when I use ACE patch in one of my proteins using FFG43a1.
> 
> I am issuing:
> pdb2gmx_3.3 -f test.pdb -ter -ignh -o test.gro
> 
> I am using -ter because I already have ACE at N terminus and NH2 at 
> C-terminus.
> 
> I used this test.gro and put it in a water box and went ahead with 
> editconf and all and finally when I made the test.tpr file using grompp 
> then it reported a warning mesg which is as follows:
> 
> warning:  [file "test.itp" , line 5010]
> No default G96Angle types, using zeroes.

this means the angle can be anything. you have to add the force constant 
and reference angle from a similar one in the rtp file (and run pdb2gmx 
again) or in your top file.

> 
> Now when I check the line 5010 it is:
> 
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            
> c2            c3
>     1     2     3     2
>     1     2     4     2    ga_18
>     3     2     4     2    ga_32
> 
> Now the first line is the line 5010 and it is nothing but the angle 
> parameter of CH3-C-O of ACE group. As is observed here no ga_ is defined 
> in front of line 5010. I also checked the .rtp file and there too this 
> angle parameter is undefined.
> 
> [ 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
>  [ impropers ]
>     C    CA    +N     O    gi_1
> 
> Although if I proceed with it then there is no problem and my 
> simulations (production run) are running fine, but I am just curious to 
> know why is this happening. I tried using difference force fields from 
> pdb2gmx but all of them give me the same problem.
> 
> Another thing is, is it correct to ignore this warning message since it 
> is for a patch only?
> 
> I shall be really thankful if I would be getting your useful suggestions 
> on this issue.
> 
> Priyanka
> 
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> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se