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<br>
the order of force field, ligand, target is correct. and usually
works fine in explicit solvent simulations.<br>
<br>
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 ..)<br>
<br>
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? <br>
<br>
btw: implicit solvent simulation with the protein only (pdb2gmx
&amber99sb parameterized) works fine ..<br>
<br>
have a nice weekend<br>
<br>
<br>
<br>
<br>
<br>
Am 04.05.2012 16:12, schrieb Alan:
<blockquote
cite="mid:CAEznbzm_iovvO4PxKZd29rsZLsjtji6CVMy2bKuXXsNMpHiy8A@mail.gmail.com"
type="cite">Have a look at <a moz-do-not-send="true"
href="http://code.google.com/p/acpype/wiki/TutorialAcpype4Gromacs">http://code.google.com/p/acpype/wiki/TutorialAcpype4Gromacs</a>
<div><br>
</div>
<div>There there's a note:</div>
<div><br>
</div>
<div><strong
style="color:rgb(0,0,0);font-family:arial,sans-serif;font-size:13px;font-style:normal;font-variant:normal;letter-spacing:normal;line-height:16px;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255)">NB(1):</strong><span
style="color:rgb(0,0,0);font-family:arial,sans-serif;font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:16px;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);display:inline!important;float:none"> </span><tt
style="font-family:Monaco,'DejaVu Sans Mono','Bitstream Vera
Sans Mono','Lucida
Console',monospace;font-size:12px;max-width:66em;color:rgb(0,0,0);font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:16px;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255)">#include
"Ligand.itp"</tt><span
style="color:rgb(0,0,0);font-family:arial,sans-serif;font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:16px;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);display:inline!important;float:none"> has
to be inserted right after </span><tt
style="font-family:Monaco,'DejaVu Sans Mono','Bitstream Vera
Sans Mono','Lucida
Console',monospace;font-size:12px;max-width:66em;color:rgb(0,0,0);font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:16px;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255)">ffamber**.itp</tt><span
style="color:rgb(0,0,0);font-family:arial,sans-serif;font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:16px;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);display:inline!important;float:none"> line
and before </span><tt style="font-family:Monaco,'DejaVu Sans
Mono','Bitstream Vera Sans Mono','Lucida
Console',monospace;font-size:12px;max-width:66em;color:rgb(0,0,0);font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:16px;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255)">Protein_*.itp</tt><span
style="color:rgb(0,0,0);font-family:arial,sans-serif;font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:16px;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);display:inline!important;float:none"> line
in </span><i
style="color:rgb(0,0,0);font-family:arial,sans-serif;font-size:13px;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:16px;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255)">Complex.top</i><span
style="color:rgb(0,0,0);font-family:arial,sans-serif;font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:16px;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);display:inline!important;float:none">.</span><br>
<br>
</div>
<div>Are you inserting your gbsa.itp in the *right* place of your
top file?</div>
<div><br>
</div>
<div>Alan</div>
<div><br>
<div class="gmail_quote">On 4 May 2012 14:14, Vedat Durmaz <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:durmaz@zib.de" target="_blank">durmaz@zib.de</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> <br>
thanks justin and alan.<br>
<br>
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".<br>
<br>
<br>
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?<br>
<br>
<br>
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.<br>
<br>
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. <br>
<br>
i can't see any correlation between the atom types listed
in my parameterized molecule's itp-file and the entries in
gbsa.itp.<br>
<br>
does anyone have any idea? is there perhaps some other
force field/database file that is checked apart from
gbsa.itp?!<br>
<br>
thanks again,<br>
<br>
vedat<br>
<br>
<br>
<br>
Am 04.05.2012 11:23, schrieb Alan:
<div>
<div class="h5">
<blockquote type="cite">Hi there,
<div><br>
</div>
<div>look at 'acpype -h', in particular:</div>
<div><br>
</div>
<div>
<div> -g, --disambiguate disambiguate lower and
uppercase atomtypes in GMX top</div>
<div> file</div>
<div><br>
</div>
<div>Alan</div>
<br>
<div class="gmail_quote">On 3 May 2012 14:34,
Vedat Durmaz <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:durmaz@zib.de" target="_blank">durmaz@zib.de</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex"> <br>
hi guys,<br>
<br>
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:<br>
<br>
GB parameter(s) missing or negative for atom
type 'cc'<br>
GB parameter(s) missing or negative for atom
type 'n'<br>
...<br>
Fatal error:<br>
Can't do GB electrostatics; the
implicit_genborn_params section of the
forcefield is missing parameters for 15
atomtypes or they might be negative.<br>
<br>
<br>
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:<br>
<br>
<br>
[ implicit_genborn_params ]<br>
<br>
; atype sar st pi gbr
hct<br>
...<br>
CC 0.172 1 1.554 0.1875
0.72 ; C<br>
<br>
<br>
does anybody know how to handle this problem?<br>
<br>
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?<br>
<br>
thanks in advance and take care<span><font
color="#888888"><br>
<br>
vedat durmaz<br>
<br>
<br>
<br>
<br>
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<div>Bioinformatician, UniProt - PANDA, EMBL-EBI<br>
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<div>
Bioinformatician, UniProt - PANDA, EMBL-EBI<br>
CB10 1SD, Hinxton, Cambridge, UK</div>
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