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

Mon Nov 26 15:43:51 CET 2012

Thank yo Justin for your help...I have generated the same topology using *ATB.
*Now, I got the masses correctly (as pointed out by you). So, I'm afraid
that is there any bug in PRODRG server?

On Mon, Nov 26, 2012 at 8:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/26/12 9:35 AM, Venkat Reddy wrote:
>
>> 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?
>>
>>
>>
> PRODRG doesn't even do a very good job of being compatible with 43A1, so
> if you re-derive the charges correctly, the result is compatible with 53A6.
>  PRODRG basically just uses 43A1 atom types, the names of which are largely
> the same in 53A6, even if the parameters are slightly different, and thus I
> view PRODRG as a method to create generic Gromos96 topologies, given that
> the user has to do a fair amount of work to create a usable topology anyway.
>
> -Justin
>
>  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
>>>>> jalemkul[at]vt.edu | (540) 231-9080
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>>>>  --
>>> ==============================****==========
>>>
>>> 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