[gmx-users] HA atom not recognised by gromacs

[Mark Abraham]

jayalakshmi sridhar wrote:
> 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.

We're not going to guess what you're doing wrong. Read editconf -h and 
experiment. If you need to ask here, to get useful help you at least 
have to give your inputs, outputs and why you thought something was wrong!

Makr

> 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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> 
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