<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY>Dear all,<br>
I am getting error while generating .gro and .top
files using pdb2gmx. I have defined my molecule in the .rtp file as
follows:<br>
<font size="1">[ PAA ]<br>
[ atoms ]<br>
HT H -0.0070 1<br>
C1 CH3 -0.2615 1<br>
C2* CH2 -0.0846 1<br>
C3 C 0.5812 1<br>
O1 OM -1.0370 1<br>
HC2 H 0.0995 1<br>
H1C1 H 0.0990 1<br>
H2C1 H 0.1411 1<br>
O2 O -0.5020 1<br>
HH H -0.0070 1<br>
[ bonds ]<br>
HT C1<br>
H1C1 C1 <br>
H2C1 C1<br>
C1 C2*<br>
HH C2*<br>
HC2 C2*<br>
C2*
C3
<br>
C3 O2<br>
C3 O1<br>
<br>
<font size="3">But when I run pdb2gmx it gives following warnings:<br>
<font size="1">WARNING: atom HH is missing in residue PAA 41 in the pdb file<br>
You might need to add atom HH to the hydrogen database of residue PAA<br>
in the file ff???.hdb (see the manual)<br>
WARNING: atom HT is missing in residue PAA 42 in the pdb file<br>
You might need to add atom HT to the hydrogen database of residue PAA<br>
in the file ff???.hdb (see the manual)<br>
WARNING: atom O1 is missing in residue PAA 42 in the pdb file<br>
WARNING: atom O1 is missing in residue PAA 42 in the pdb file<br>
WARNING: atom HH is missing in residue PAA 42 in the pdb file<br>
You might need to add atom HH to the hydrogen database of residue PAA<br>
in the file ff???.hdb (see the manual)<br>
WARNING: atom HT is missing in residue PAA 43 in the pdb file<br>
You might need to add atom HT to the hydrogen database of residue PAA<br>
in the file ff???.hdb (see the manual)<br>
WARNING: atom O1 is missing in residue PAA 43 in the pdb file<br>
WARNING: atom O1 is missing in residue PAA 43 in the pdb file<br>
</font></font></font>continued......<br>
<br>
When I run the command--<br>
pdb2gmx -f ....pdb -o ...gro -p ...top -ter -missing<br>
<br>
it generates the .gro and .top files but in both the files it takes
only one oxygen and that also just O. What may be the problem?<br>
Thanking you in advance.<br>
<br>
Rahul Karyappa<br>
NCL, Pune<br>
<br>
<br>
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