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On 2/06/2012 7:10 PM, xi zhao wrote:
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<div>Dear gmx-users:</div>
<div>When I try to simulation a system: protein + ligand
molecule using the Implicit Solvent method. the
parameters of Ligand were produced by acpype, but when
grompped, the appeared" </div>
<div>" Velocities were taken from a Maxwell distribution
at 300 K</div>
<div>GB parameter(s) missing or negative for atom type 'o'</div>
<div>GB parameter(s) missing or negative for atom type
'os'</div>
<div>GB parameter(s) missing or negative for atom type 'c'</div>
<div>GB parameter(s) missing or negative for atom type
'c3'</div>
<div>GB parameter(s) missing or negative for atom type
'hc'</div>
<div>GB parameter(s) missing or negative for atom type
'h1'</div>
<div>-------------------------------------------------------<br>
Program grompp_d, VERSION 4.5.3<br>
Source code file: grompp.c, line: 1123</div>
<div>Fatal error:<br>
Can't do GB electrostatics; the implicit_genborn_params
section of the forcefield is missing parameters for 6
atomtypes or they might be negative."</div>
<div>when I modified "<a moz-do-not-send="true"
class="plink"
href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844"
rel="nofollow" target="_blank"><img
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src="http://opi.yahoo.com/online?u=zhaoxiitc2002&t=4&l=cn"
border="0"></a>amber99sbr.ff/gbsa.itp by adding the
atomtype of ligand, the problem is still the same, </div>
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<br>
Then you apparently didn't add them correctly. See manual section
5.3.5 and second paragraph of <a
href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a><br>
<br>
Mark<br>
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