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

[Justin Lemkul]

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
>>>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>>> <h**ttp://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<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

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