[gmx-users] GB parameter(s) missing or negative but they aint missing nor negative

[Gert Peters]

Dear all,

Im trying to run an md or em using an implicit solvation method using 
gromacs 4.5.5 but I allways get the same errors.


GB parameter(s) missing or negative for atom type 'OS'

GB parameter(s) missing or negative for atom type 'H2'

GB parameter(s) missing or negative for atom type 'N*'

GB parameter(s) missing or negative for atom type 'CK'

GB parameter(s) missing or negative for atom type 'P'

---
Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 1123

Fatal error:
Can't do GB electrostatics; the implicit_genborn_params section of the 
forcefield is missing parameters for 5 atomtypes or they might be negative.


Istart from default.pdb (41bp RNA) and perform following:

pdb2gmx -f default.pdb -ff amber03 -water none -ignh
editconf -f conf.gro -d 2 -bt triclinic -c
grompp -f em_gbis.mdp -c out.gro

with em_gbis.mdp containing:

integrator= steep
nsteps= -1
nstlist= 10
emstep=1
rlist= 2.0
coulombtype= cut-off
rcoulomb= 2.0
vdw-type= cut-off
rvdw= 2.0
nstenergy= 10
implicit_solvent = GBSA
constraints=none
rgbradii=2.0
gb_algorithm=OBC
sa_algorithm=Ace-approximation

Now the odd part is that I added all missing parameters to the 
/gromacs-4.5.5/share/top/amber...ff/gbsa.itp for example for H2:


...
H4   0.1  1  10.115 0.85 ; H
H5   0.1  1  10.125 0.85 ; H
H2   0.1  1  10.125 0.85 ; H
...

I tried doing this for amber 94, 99 and 03 but allways the same result.

Anyone got a clue? I dont think I did something wrong as the implicit 
solvation model previously worked. All input is appreciated.


Thanks in advance,
Gert
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[gmx-users] Dangling bond at terminal end of RNA rosetta model

[Gert Peters]

Hi everybody,

Im trying to use GROMACS for MD of a RNA model generated by Rosetta 
(FARFAR). As a test I try processing a modelledpdb file. When I prepare 
thetopology files (pdb2gmx -f test.pdb -ff amber99 -ignh

) from pdb I encounter following output :

Sorting it all out...
Opening force field file 
/usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.hdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/amber99.ff/dna.hdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/amber99.ff/rna.hdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.n.tdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.c.tdb


Back Off! I just backed up topol.top to ./#topol.top.12#
Processing chain 1 'A' (165 atoms, 8 residues)
Identified residue rG1 as a starting terminus.
Identified residue rC8 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully

---
Program pdb2gmx, VERSION 4.5.5
Source code file: pdb2top.c, line: 1031

Fatal error:
There is a dangling bond at at least one of the terminal ends and the 
force field does not provide terminal entries or files. Edit a .n.tdb 
and/or .c.tdb file.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


When processing the corresponding structure from the pdb database 
(2IXZ)all files are generated as expected. I tried to compare the de 
novo model with the experimentally determined one but I cant find the 
problem(all terminal residues seem to have the same amountof atoms when 
ignoring the hydrogen atoms). I dont have a clue where to look next.


Anyone got a clueto solve this issue?

Thanks in advance,

Kind regards,
Gert
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