[gmx-users] missing gbsa parameters
Vedat Durmaz
durmaz at zib.de
Fri May 4 18:36:07 CEST 2012
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 <durmaz at zib.de
> <mailto:durmaz at 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 <durmaz at zib.de
>> <mailto:durmaz at 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
>>
>>
>>
>>
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>>
>> --
>> 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>
>>
>>
>>
>
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>
>
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Bioinformatician, UniProt - PANDA, EMBL-EBI
> CB10 1SD, Hinxton, Cambridge, UK
> +44 1223 49 4588
>
>
>
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