I know it's much better to use a non-deprecated ff. But what could I do? I have to regenerate the results of simulation done by gmx.ff . Aren't there any solution to pass this step?
I PROMISE YOU AND ME TO REPEAT THE SIMULATION WHIT A MODERN FF AS SOON AS POSSIBLE :) Sincerely, Shima ----- Original Message ----- From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Wednesday, June 27, 2012 9:55 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 12:50 PM, Shima Arasteh wrote: > OK. > PDB FILE IS AS BELOW: > > HETATM 1 C FOR 0 -0.721 1.600 1.249 > HETATM 2 O FOR 0 -0.839 2.806 1.453 > ATOM 3 N VAL 1 -1.227 0.728 2.125 > ATOM 4 CA VAL 1 -1.918 1.159 3.323 > ATOM 5 C VAL 1 -1.969 2.678 3.410 > ATOM 6 O VAL 1 -0.931 3.335 3.447 > ATOM 7 CB VAL 1 -1.219 0.644 4.576 > ATOM 8 CG1 VAL 1 0.208 1.178 4.618 > ATOM 9 CG2 VAL 1 -1.976 1.118 5.812 > ATOM 10 N SER 2 -3.181 3.235 3.442 > ATOM 11 CA SER 2 -3.363 4.671 3.524 > ATOM 12 CB SER 2 -4.138 5.196 2.320 > ATOM 13 OG SER 2 -4.296 6.612 2.437 > ATOM 14 C SER 2 -4.135 5.054 4.778 > ATOM 15 O SER 2 -5.272 4.628 4.966 > > The error comes from the VAL residue (residue 2 in the sequence based on the internal numbering used by pdb2gmx, as I suspected earlier). Note the following line in the [impropers] section of aminoacids.rtp in the [VAL] entry: -C -CA N -O The improper is defined using the position of a CA atom in the preceding residue, which in this case does not exist because it is not a normal amino acid (though an ACE cap will also work because its atoms are named suitably). This method of defining the improper is somewhat odd. Using a more modern force field like Gromos96 53a6 does not give rise to this error, as all impropers are defined using only -C or +N. Just another reason to use a non-deprecated force field :) -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
