[gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

[Venkat Reddy]

Dear Justin,
One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate
topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I
mix 53A6 and 43A1?


On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/26/12 9:12 AM, Venkat Reddy wrote:
>
>> Dear Justin,
>> I haven't touched the *Mass column.* I have edited the charges only using
>> "gedit" in linux.
>>
>>
> Regardless, the masses I pointed out are wrong.  You should still do the
> test to #include the original topology and see if it works, then if it
> does, figure out the source of the error in your file.
>
> -Justin
>
>
>> On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 11/26/12 12:58 AM, Venkat Reddy wrote:
>>>
>>>  Dear all,
>>>> I am simulating a Protein-Drug complex. I am following Justin's
>>>> tutorial.
>>>> I
>>>> have used *PRODRG *for generating topology. *Gaussian *has given me the
>>>> ESP
>>>> charges. I have edited the charges in the itp file using the
>>>> *Gaussian*'s
>>>> ESP charges*. *Then I am getting this strange error.
>>>>
>>>>    *ERROR 1 [file protein.top, line 75]:*
>>>> *  atom C4 (Res ORP-1) has mass 0*
>>>> *
>>>> *
>>>> *
>>>> *
>>>> *
>>>> *
>>>> *ERROR 2 [file protein.top, line 75]:*
>>>> *  atom C14 (Res ORP-1) has mass 0*
>>>>
>>>>
>>>>  Probably there are some hidden line ending problems.  Did you edit the
>>> file with a plain text editor?
>>>
>>> Also note...
>>>
>>>        24       CH2     1  ORP      C5     4    0.354  13.0190
>>>
>>>>       *25       CH1     1  ORP      C4     4   -0.024  14.0270*
>>>>
>>>>
>>> These masses don't make sense.  CH2 should have a mass of 14.027 and CH1
>>> should have a mass of 13.019.  I've never seen PRODRG get something like
>>> this wrong; were you sure to carefully change the file?  It seems
>>> something
>>> has gone very wrong here.
>>>
>>> Compare the original topology (from PRODRG) with the one you edited.  If
>>> grompp succeeds using the PRODRG topology (stop using it after that
>>> point),
>>> then the error arose due to something you did when editing the file.
>>>
>>> -Justin
>>>
>>> --
>>> ==============================****==========
>>>
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
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> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036