[gmx-users] Atom N not found....
rama david
ramadavidgroup at gmail.com
Fri Apr 6 14:04:31 CEST 2012
Hi GROMACS Friends and Mark..
Thank you for reply ...
My command line is
pdb2gmx -f ....pdb -o p.pdb -p p.top -ignh -ter
I choose the G96 53a6 ff , along with spc water model.
Select start terminus type for ACE-1
0: NH3+
1: NH2
2: None
2
Start terminus ACE-1: None
Select end terminus
0: COO-
1: COOH
2: None
0
End terminus : COO-
So I got the following out put...
Program pdb2gmx, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2gmx.c, line:
655
Fatal error:
Atom CH3 in residue ACE 1 was not found in rtp entry ACE with 3 atoms
while sorting atoms.
.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
I have the limited experience for these problem..
Can you tell me what to do in such conditions????
I change the Atom CH3 in pdb to CA and proceed with the above command line
and option .
I got the following error
Program pdb2gmx, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/kernel/resall.c, line: 581
Fatal error:
Residue 'CE' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
I have the limited experience for these problem..
Can you tell me what to do in such conditions????
On Fri, Apr 6, 2012 at 4:38 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> On 6/04/2012 9:05 PM, Mark Abraham wrote:
>
> On 6/04/2012 8:27 PM, rama david wrote:
>
> Hi Gromacs Friends and Justin ,
>
> Thank you for reply and suggestion.
>
> These is short part of my PDB .
>
> ATOM 1 1H ACE 1 0.000 0.000 0.000
> ATOM 2 CH3 ACE 1 0.000 1.090 0.000
> ATOM 3 2H ACE 1 1.028 1.453 -0.000
> ATOM 4 3H ACE 1 -0.514 1.453 -0.890
> ATOM 5 C ACE 1 -0.721 1.600 1.249
> ATOM 6 O ACE 1 -0.839 2.806 1.453
> ATOM 7 N PRO 2 -1.227 0.727 2.126
> ATOM 8 CA PRO 2 -1.918 1.181 3.321
> ATOM 9 HA PRO 2 -2.553 2.031 3.073
> ATOM 10 C PRO 2 -0.928 1.587 4.404
> ATOM 11 O PRO 2 -1.069 2.645 5.013
> ATOM 12 CB PRO 2 -2.782 0.075 3.851
> ATOM 13 1HB PRO 2 -2.469 -0.177 4.864
> ATOM 14 2HB PRO 2 -3.822 0.401 3.862
> ATOM 15 CG PRO 2 -2.645 -1.140 2.964
> ATOM 16 1HG PRO 2 -2.232 -1.966 3.542
> ATOM 17 2HG PRO 2 -3.606 -1.451 2.556
> ATOM 18 CD PRO 2 -1.680 -0.755 1.882
> ATOM 19 1HD PRO 2 -2.173 -0.830 0.913
> ATOM 20 2HD PRO 2 -0.816 -1.419 1.895
> ATOM 21 N GLY 3 0.076 0.740 4.644
> ATOM 22 H GLY 3 0.135 -0.114 4.109
> ATOM 23 CA GLY 3 1.083 1.012 5.650
>
> The gromacs96 53a6 .rtp file mention the following data...
>
> bondedtypes ]
> ; bonds angles dihedrals impropers
> 2 2 1 2
>
> [ ACE ]
> [ atoms ]
> CA CH3 0.000 0
> C C 0.450 1
> O O -0.450 1
> [ bonds ]
> C CA gb_27
> C O gb_5
> C +N gb_19
> [ angles ]
> CA C O ga_30
> CA C +N ga_19
> O C +N ga_33
> [ impropers ]
> C CA +N O gi_1
>
> [ NH2 ]
> [ atoms ]
> N NT -0.83 0
> H1 H 0.415 0
> H2 H 0.415 0
> [ bonds ]
> N H1 gb_2
> N H2 gb_2
> -C N gb_9
> [ angles ]
> -O -C N ga_33
> -CA -C N ga_19
> -C N H1 ga_23
> -C N H2 ga_23
> H1 N H2 ga_24
> [ dihedrals ]
> -CA -C N H1 gd_14
> [ impropers ]
> -C -O N -CA gi_1
> N H1 H2 -C gi_1
>
> As per my pdb file N atom is the part of PROLINE , not the ACE...
> I got the topology by using the Amber 03 FF.
> But my priority is to the GROMOS96 53a6 force field ...
>
> Could any suggest me the way to tackle these problem???
>
>
> The default is to try to put termini on the protein chain. Your chain
> already has them, so you need to tell pdb2gmx not to try to add termini.
> See pdb2gmx -h.
>
>
> ... and if you'd also shown the last piece of your pdb2gmx output and
> given us the whole command line you used, then you'd have gotten your
> answer faster and wasted less of people's time guessing what the real
> problem was.
>
> Mark
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120406/428d6a84/attachment.html>
More information about the gromacs.org_gmx-users
mailing list