Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private tutor. I am CC'ing the list and ask that further comments and
questions will be posted there.
On 2/25/13 9:09 AM, bhavaniprasad vipperla wrote:
Hello sir,
I have been using GROMACS for my MD work. I had many queries cleared by you
earlier.
I got a query, please help me out regarding this.
I am trying to do MD study for a phosphorylated and un-phosphorylated form of
my protein.
I have tried adding the phosphate group using Discovery studio but it doesn't
get read as Phosphotyrosine while running in gromacs.
I had obtained the modified forcefields submitted by you, having
Phosphorylated versions of the Aminoacids from the gromacs website and using it
for simulations.
Its giving an error
Warning: Residue PTR208 in chain has different type(other) from starting
residue MET1 (Protein)
Identified Residue ASN207 as a ending terminus.
The above warnings are fixed by following step 5 here:
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue
*Fatal Error:*
*Residue 'HISE' not found in residue topology database.*
*
*
But i dont have any HISE residue in my topology and its also not reading the
phosphorylated residue at 208 position.
I tried checking in the gromacs forum, but couldnt find any related queries. So
am asking for your help.
Here, you probably need to add an entry in aminoacids.r2b to translate building
block and .rtp names. HISE is the epsilon-protonated form of histidine, which
is called HISB in many force fields. See existing force field files for an example.
-Justin
--
========================================
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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