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

[Justin Lemkul]

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
>> 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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>
>
>

-- 
========================================

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

========================================