<b>Dear gmx-users, <br>I am trying to insert a custom residue (a phosphoserine) in Gromacs using force field Amber ff99sb-ildn.<br>I created a new .rtp entry named SEP like this:</b><br><br>[SEP]<br> [ atoms ]<br> N N -0.49370 1<br>
H H 0.30180 2<br> CA CT -0.23800 3<br> HA H1 0.09370 4<br> CB CT 0.07820 5<br> HB1 H1 -0.06020 6<br> HB2 H1 -0.06020 7<br>
OG OS -0.55930 8<br> PS P 1.40000 9<br> OPA O2 -0.85000 10<br> OPB O2 -0.85000 11<br> OPC O2 -0.85000 12<br> C C 0.67310 13<br>
O O -0.58540 14<br> [ bonds ]<br> N H<br> N CA<br> CA HA<br> CA CB<br> CA C<br> CB HB1<br> CB HB2<br> CB OG<br> OG PS<br> PS OPA<br> PS OPB<br>
PS OPC<br> C O<br><br><b>After that, I got this error:</b><br><br>WARNING: atom H is missing in residue SEP 124 in the pdb file<br> You might need to add atom H to the hydrogen database of building block SEP<br>
in the file aminoacids.hdb (see the manual)<br><br><br>WARNING: atom HA is missing in residue SEP 124 in the pdb file<br> You might need to add atom HA to the hydrogen database of building block SEP<br> in the file aminoacids.hdb (see the manual)<br>
<br><br>WARNING: atom HB1 is missing in residue SEP 124 in the pdb file<br> You might need to add atom HB1 to the hydrogen database of building block SEP<br> in the file aminoacids.hdb (see the manual)<br>
<br><br>WARNING: atom HB2 is missing in residue SEP 124 in the pdb file<br> You might need to add atom HB2 to the hydrogen database of building block SEP<br> in the file aminoacids.hdb (see the manual)<br>
<br><br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 4.5.3<br>Source code file: pdb2top.c, line: 1449<br><br>Fatal error:<br>There were 4 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology anyhow, use the option -missing<br>
For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>-------------------------------------------------------<br>
<b><br><br>So, I modified aminoacids.hdb adding a new entry for SEP:</b><br><br>SEP 4<br>1 1 H N -C CA<br>1 5 HA CA N CB C<br>2 4 HB CB CA N<br>
<b><br>but when I tried to use pdb2gmx in order to create .gro and .top files I got the following error:</b><br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 4.5.3<br>Source code file: h_db.c, line: 174<br>
<br>Fatal error:<br>Error reading from file /usr/local/gromacs/share/gromacs/top//amber99sb-ildn.ff/aminoacids.hdb<br>For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
_______________________________<br><br><b>This is not making any sense to me, since the file is still there, and the only change was the new SEP entry...</b><br>I appreciate any help you could give!<br>Best regards<br> Alberto<br>
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