[gmx-users] Error in generating a gromacs structure file for Arginine
Dallas Warren
dallas.warren at monash.edu
Wed Jun 5 00:05:02 CEST 2019
Have you looked at the residue database file? aminoacids.rtp That is
what the error is telling you to do, ensure that your residue(s) match
up with what is in the residue database.
First off, atom type OXT is not in any of the arginine residues listed
there. Second you have a choice of three arginine residues, ARG, CARG
NARG. Your amino acid molecule doesn't fall into any of those. You
probably need to use CARG with a NH2 residue, I think that will get
you what you want. Check to see that the atom and residue names in
your pdb match up with the entries in the aminoacids.rtp, then should
be good to go.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
On Wed, 5 Jun 2019 at 02:54, Pandya, Akash <akash.pandya.15 at ucl.ac.uk> wrote:
>
> Hi all,
>
> I'm trying to run MD simulations with Arginine. I'm using the AMBER99SB-ILDN FF and I get this error:
>
> There is a dangling bond at at least one of the terminal ends and the force
> field does not provide terminal entries or files. Fix your terminal residues
> so that they match the residue database (.rtp) entries, or provide terminal
> database entries (.tdb).
>
> I've tried to search the error but don't know what I have done wrong? I used the command below:
>
> gmx pdb2gmx -f Arg.pdb -o Arg.gro -water tip3p
>
> The Arg.pdb looks like this:
>
> COMPND Arginine
> AUTHOR GENERATED BY OPEN BABEL 2.3.90
> ATOM 1 O Arg A 1 -2.303 -1.954 -0.204 1.00 0.00 O
> ATOM 2 OXT Arg A 1 -3.444 -0.531 1.147 1.00 0.00 O
> ATOM 3 N Arg A 1 -2.892 1.602 -0.334 1.00 0.00 N
> ATOM 4 NE Arg A 1 1.964 -0.236 0.050 1.00 0.00 N
> ATOM 5 NH1 Arg A 1 3.918 -1.417 -0.350 1.00 0.00 N
> ATOM 6 NH2 Arg A 1 4.137 0.763 0.281 1.00 0.00 N
> ATOM 7 CB Arg A 1 -0.770 0.493 -0.870 1.00 0.00 C
> ATOM 8 CG Arg A 1 -0.171 0.875 0.492 1.00 0.00 C
> ATOM 9 CA Arg A 1 -2.299 0.356 -0.813 1.00 0.00 C
> ATOM 10 CD Arg A 1 1.345 1.033 0.437 1.00 0.00 C
> ATOM 11 C Arg A 1 -2.746 -0.721 0.159 1.00 0.00 C
> ATOM 12 CZ Arg A 1 3.260 -0.263 0.006 1.00 0.00 C
> ATOM 13 HB1 Arg A 1 -0.337 -0.454 -1.215 1.00 0.00 H
> ATOM 14 HB2 Arg A 1 -0.499 1.254 -1.613 1.00 0.00 H
> ATOM 15 HG1 Arg A 1 -0.595 1.821 0.847 1.00 0.00 H
> ATOM 16 HG2 Arg A 1 -0.419 0.109 1.237 1.00 0.00 H
> ATOM 17 HA Arg A 1 -2.702 0.120 -1.804 1.00 0.00 H
> ATOM 18 HD1 Arg A 1 1.601 1.820 -0.282 1.00 0.00 H
> ATOM 19 HD2 Arg A 1 1.695 1.340 1.430 1.00 0.00 H
> ATOM 20 H1 Arg A 1 -3.908 1.542 -0.388 1.00 0.00 H
> ATOM 21 H2 Arg A 1 -2.621 2.369 -0.949 1.00 0.00 H
> ATOM 22 H Arg A 1 -2.603 -2.648 0.421 1.00 0.00 H
> ATOM 23 HH11 Arg A 1 3.406 -2.261 -0.582 1.00 0.00 H
> ATOM 24 HH12 Arg A 1 4.931 -1.459 -0.390 1.00 0.00 H
> ATOM 25 HH21 Arg A 1 5.140 0.625 0.213 1.00 0.00 H
> ATOM 26 HH22 Arg A 1 3.821 1.686 0.556 1.00 0.00 H
>
> CONECT 1 11 22
> CONECT 2 11
> CONECT 3 9 20 21
> CONECT 4 10 12
> CONECT 5 12 23 24
> CONECT 6 12 25 26
> CONECT 7 8 9 13 14
> CONECT 8 7 10 15 16
> CONECT 9 3 7 11 17
> CONECT 10 4 8 18 19
> CONECT 11 1 2 9
> CONECT 12 4 5 6
> CONECT 13 7
> CONECT 14 7
> CONECT 15 8
> CONECT 16 8
> CONECT 17 9
> CONECT 18 10
> CONECT 19 10
> CONECT 20 3
> CONECT 21 3
> CONECT 22 1
> CONECT 23 5
> CONECT 24 5
> CONECT 25 6
> CONECT 26 6
> MASTER 0 0 0 0 0 0 0 0 26 0 26 0
> END
>
> Please advise me on how to solve this error.
>
>
> Akash
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