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

[Venkat Reddy]

Dear Justin,
I haven't touched the *Mass column.* I have edited the charges only using
"gedit" in linux.


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
> 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