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 <jalem...@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 <jalem...@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 <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
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