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Hi,<br><br>I fixed it for the next beta release.<br>If you need it now, change on line 1574 (my latest version) of src/kernel/pdb2gmx.c<br>cc->r_start to cc->r_end, or get the 4.5 version from git.<br><br>Berk<br><br>Date: Tue, 24 Aug 2010 09:21:44 -0500<br>From: kkuczera@ku.edu<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] Incorrect C-terminal in peptide starting with GLY<br><br><pre>Hi gmx-users<br>I am trying to set up a simulation of a 16-residue peptide that starts <br>with GLY and ends with GLU<br>(PDB attached) using OPLS-AA/L and gromacs-4.5-beta3. Here is the <br>pdb2gmx command<br> <br>pdb2gmx -inter -ignh -f b-hp41-56.pdb -p peptide.top -o peptide.gro<br> <br>the ff, water, ionization state selection goes well,<br> I get a selection of N-terminals that includes GLY-NH3+ which is fine<br>but then the selection of C-terminals does not have COO-, but only GLY-COO-<br>- as a result the C-terminal GLU ends up with incorrect charge and qtot <br>is not an integer<br> <br>Without the '-inter', the system gets GLY-NH3+ and GLY-COO- as well ...<br> <br>Could someone suggest a fix for this ?<br> <br>Regards<br>Krzysztof<br> <br>-- <br>Krzysztof Kuczera<br>Departments of Chemistry and Molecular Biosciences<br>The University of Kansas<br>2010 Malott Hall<br>Lawrence, KS 66045<br>Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera@ku.edu<br><a href="http://oolung.chem.ku.edu/%7Ekuczera/home.html" target="_blank">http://oolung.chem.ku.edu/~kuczera/home.html</a><br> <br> <br></pre><br>--
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