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 <jalem...@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.
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Department of Biochemistry
Virginia Tech
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jalemkul[at]vt.edu | (540) 231-9080
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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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