[gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0
jalemkul at vt.edu
Mon Nov 26 15:05:16 CET 2012
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?
> 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
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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