[gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0
Justin Lemkul
jalemkul at vt.edu
Mon Nov 26 15:48:36 CET 2012
On 11/26/12 9:43 AM, Venkat Reddy wrote:
> 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?
>
>
I have no idea. I haven't used PRODRG in a very long time.
-Justin
> 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
>>>>>> http://www.bevanlab.biochem.******vt.edu/Pages/Personal/justin**<
>>>>>> http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin>
>>>>>>>
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>>>>>>>
>>>>>>
>>>>>>>
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>>>>>>
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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://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
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