[gmx-users] Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms

[Nilesh Dhumal]

I have addes the "CO" residue.
Coordinate file

REMARK   Accelrys Discovery Studio PDB file
REMARK   Created:  Fri May 28 17:26:23 Eastern Daylight Time 2010
HETATM    1  C1  CO     0      -1.044  -0.027   0.066  0.00  0.00           C
HETATM    2  O2  CO     0      -0.009   0.642  -0.037  0.00  0.00           O
HETATM    3  O3  CO     0      -2.286   0.595  -0.030  0.00  0.00           O
END

in ffopla.rtp file.

[ CO ] ; mandatory
[ ATOMS ] ; mandatory
 C1   opls_974    1.00   1
 O2   opls_975   -0.50   2
 O3   opls_976   -0.50   2

[ bonds ]
 C1 O2
 C1 O3

I have also addes new atoms typs in ffopls.atp file.

NIlesh

On Tue, June 1, 2010 3:35 pm, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> Hello,
>>
>>
>> I am getting the following error during pdb2gmx.
>>
>>
>> Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms
>>  while sorting atoms
>>
>> I checked the pdb file and ffopls.rtp file also.
>>
>>
>
> And what did you find?  To my knowledge there is no such residue "CO" in
> the ffoplsaa.rtp file.  Is this something you've added?  Regardless,
> there's a mismatch somewhere, so if you can't identify it, post the text
> of your coordinate file and the relevant .rtp entry to see if someone else
> can spot it.
>
> -Justin
>
>
>> Nilesh
>>
>>
>>
>>
>>
>
> --
> ========================================
>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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 at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>
>
>