Have a look at <a 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 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 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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<br>
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<div><br>
</div>
-- <br>
Alan Wilter SOUSA da SILVA, DSc
<div>Bioinformatician, UniProt - PANDA, EMBL-EBI<br>
CB10 1SD, Hinxton, Cambridge, UK</div>
<div><a href="tel:%2B44%201223%2049%204588" value="+441223494588" target="_blank">+44 1223 49 4588</a></div>
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<fieldset></fieldset>
<br>
</blockquote>
</div></div></div>
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Bioinformatician, UniProt - PANDA, EMBL-EBI<br>CB10 1SD, Hinxton, Cambridge, UK</div><div>+44 1223 49 4588</div><br>
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