[gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0
venkat4bt at gmail.com
Mon Nov 26 15:12:17 CET 2012
I haven't touched the *Mass column.* I have edited the charges only using
"gedit" in linux.
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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With Best Wishes
Venkat Reddy Chirasani
Laboratory of Computational Biophysics
Department of Biotechnology
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