[gmx-users] missing gbsa parameters

Justin A. Lemkul jalemkul at vt.edu
Fri May 4 16:06:55 CEST 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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