[gmx-users] missing gbsa parameters

[Justin A. Lemkul]

On 5/4/12 9:44 AM, Vedat Durmaz wrote:
>
> yes, i do understand this. but what i really do not get is that grompp fails
> telling me "GB parameter(s) missing or negative for atom type 'C'", ALTHOUGH 'C'
> is listed in gbsa.itp.
>
> thus, from 15 atom types reportedly lacking gb parameters according to grompp,
> about 10 ARE listed in gbsa.itp.
>
> any idea what might cause that?
>
>

Not really.  That's very strange.  Looking at the amber*.ff/gbsa.itp files, it 
seems all of them start with a commented line (;H0 or ;Br) except for amber03, 
whose first line is for C.

It would be really weird if something was going wrong with simple line parsing, 
but you could try to make a local copy of amber99sb.ff/ and edit gbsa.itp to 
remove the commented line to see if it changes anything.  I only wonder because 
C is the first atom type in each file after the commented line, maybe something 
is not being parsed properly.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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