[gmx-users] HA atom not recognised by gromacs

[jayalakshmi sridhar]

Thankyou. I was able to get .gro file. How can I specify a octahedron box
for solvation. I am unable to get the syntax of the command right with -box
and -bt.
Jaya

On Fri, Sep 11, 2009 at 10:52 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> jayalakshmi sridhar wrote:
>
>> Dear Gromacs users,
>> I have a homology model of a protein. Te N-terminal is an ASP residue.
>> When I run the command
>> pdb2gmx -f protein.pdb -o protein.gro -ff G43a1 -p protein.top -i
>> posre.itp
>> I get the following error-
>> Atom HA in residue ASP 1 not found in rtp entry with 9 atoms
>>             while sorting atoms. Maybe different protonation state.
>>             Remove this hydrogen or choose a different protonation state.
>>             Option -ignh will ignore all hydrogens in the input.
>> The protein looks alright in Sybyl. How to get this working? Thanks for
>> the help.
>>
>
> G43a1 is a united-atom force field.  Alpha-carbons are not explicitly
> represented.  So if you pass this structure to pdb2gmx, the program assumes
> you have only the necessary atoms present.  If you have unnecessary
> hydrogens, use -ignh.
>
> -Justin
>
>  Jaya
>>
>>
>> ------------------------------------------------------------------------
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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