[gmx-users] Re: Regarding Gromacs error

[Justin Lemkul]

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

-- 
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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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