[gmx-users] ACE patch in FFG43a1
David van der Spoel
spoel at xray.bmc.uu.se
Fri Aug 8 07:47:08 CEST 2008
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
> 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.
> Unlimited freedom, unlimited storage. Get it now
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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
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