[gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0
jalemkul at vt.edu
Mon Nov 26 15:16:37 CET 2012
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.
> 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.
>>> have used *PRODRG *for generating topology. *Gaussian *has given me the
>>> 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 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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