[gmx-users] CL atom not being recognised

[jayant james]

Hi!
I am using the gromos9643a1 forcefield and the chloride is described as
given below in the rtp file. I have described the CL as CL- in my pdb input
file and still it is not accepting! I am using V 4.0.5

[ CL- ]
 [ atoms ]
   CL   CL-    -1.00000     0
 [ bonds ]
 [ angles ]
;  ai    aj    ak   gromos type
 [ impropers ]
;  ai    aj    ak    al   gromos type
 [ dihedrals ]
;  ai    aj    ak    al   gromos type


On Mon, Jun 28, 2010 at 4:15 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> jayant james wrote:
>
>> Hi!
>> The protein I am attempting to simulate has a CL atom. When I run pdb2gmx
>> I get the following error message. Any help in overcoming this problem would
>> be appreciated.
>> Thanks
>> James ------------------------------------------------------
>> Program pdb2gmx, VERSION 4.0
>> Source code file: pdb2gmx.c, line: 429
>>
>> Fatal error:
>> Atom CL- in residue CL- 574 not found in rtp entry with 1 atoms
>>             while sorting atoms
>> -------------------------------------------------------
>>
>
> You haven't told us which force field you're trying to use, but I'm
> guessing that the chloride .rtp entry is probably named "CL" instead of
> "CL-" (which is used by the ffG* force fields).  You can check the .rtp file
> to be sure.
>
> Also, I would strongly suggest upgrading to version 4.0.7 - there have been
> numerous bug fixes and performance upgrades since version 4.0.
>
> -Justin
>
>
>>
>> --
>> Jayasundar Jayant James
>>
>> www.chick.com/reading/tracts/0096/0096_01.asp <
>> http://www.chick.com/reading/tracts/0096/0096_01.asp>)
>>
>>
> --
> ========================================
>
> 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
>
> ========================================
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-- 
Jayasundar Jayant James

www.chick.com/reading/tracts/0096/0096_01.asp)
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