the order of force field, ligand, target is correct. and usually works
fine in explicit solvent simulations.
but i actually do not include the gbsa.itp, since it is defined by the
choice of the force field. (as soon as i rename its gbst.itp, grompp
says it cannot find that file ..)
but in general: so far, i always used the standard value for the "-a"
option of acpype. however, in order to do implicit simulations with
amber99sb, which setting (gaff or amber) do i have to use, alan? are
both valid?
btw: implicit solvent simulation with the protein only (pdb2gmx
&amber99sb parameterized) works fine ..
have a nice weekend
Am 04.05.2012 16:12, schrieb Alan:
Have a look at
http://code.google.com/p/acpype/wiki/TutorialAcpype4Gromacs
There there's a note:
*NB(1):*#include "Ligand.itp" has to be inserted right after
ffamber**.itp line and before Protein_*.itp line in /Complex.top/.
Are you inserting your gbsa.itp in the *right* place of your top file?
Alan
On 4 May 2012 14:14, Vedat Durmaz <dur...@zib.de
<mailto:dur...@zib.de>> wrote:
thanks justin and alan.
i also had the suspicion that the error is caused by case
sensitivity. simply replacing all atom types from lower to upper
case within the ligand.itp file yields the same error: "missing gb
parameters".
using the "--disambiguate" option for the parameterization with
acpype has exactly no effect. the generated *_GMX.itp file still
contains the same lower case letters for each atom type. am i
doing something wrong?
when using the "-atom amber" option (amber99sb instead of gaff), i
do get upper case types, which are not always the same as given
with "-a gaff". however, again, i am told by grompp, that GB
parameters are missing for 15 atom types. and again, most of
theese atom types ARE included in the respective gbsa.itp file (in
share/gromacs/top/amber99sb.ff), but few are not.
and according to those atom types that are not mentioned in
grompp's error output: about half of them is listed in gbsa.itp
while the other ones are not.
i can't see any correlation between the atom types listed in my
parameterized molecule's itp-file and the entries in gbsa.itp.
does anyone have any idea? is there perhaps some other force
field/database file that is checked apart from gbsa.itp?!
thanks again,
vedat
Am 04.05.2012 11:23, schrieb Alan:
Hi there,
look at 'acpype -h', in particular:
-g, --disambiguate disambiguate lower and uppercase atomtypes
in GMX top
file
Alan
On 3 May 2012 14:34, Vedat Durmaz <dur...@zib.de
<mailto:dur...@zib.de>> wrote:
hi guys,
i'm trying to simulate some receptor ligand system with
implicit solvent using gbsa in order to get a quick folding
of some tens of N-terminal peptides. this works pretty well
with the target only applying the amber99sb FF. as soon as i
try to simulate it together with the ligand which was
parameterized with acpype (using amber-antechamber), i get
the following error at the grompp step:
GB parameter(s) missing or negative for atom type 'cc'
GB parameter(s) missing or negative for atom type 'n'
...
Fatal error:
Can't do GB electrostatics; the implicit_genborn_params
section of the forcefield is missing parameters for 15
atomtypes or they might be negative.
the atom types in the error output are exactly those listed
in the [ atom types ] section of the ligand's topology file
created with acpype/antechamber. however, the atom types
mentioned here ARE listed in the respective gbsa.itp file
which looks like this:
[ implicit_genborn_params ]
; atype sar st pi gbr hct
...
CC 0.172 1 1.554 0.1875 0.72 ; C
does anybody know how to handle this problem?
and is there someone that can tell me how (with which
parameter values) to add GAFF atom types like e.g. "ss",
"hn", "hx", "os" to the gbsa.itp file?
thanks in advance and take care
vedat durmaz
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588 <tel:%2B44%201223%2049%204588>
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
