<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>
Hi I am running a mdrun on one polymer chain. I have
entered all the atoms and atom types in .rtp file. But while running
pdb2gmx command it gives one error that atom O is not entered in the
.rtp file. Actually there are two O atoms which are given in .pdb as
O1- and O2. I have mentioned the same atoms. But it asks for O atom
which is not there in the .pdb file. What should I do? Where am I going
wrong?<br>
In the .rtp file I have mentioned atoms for only one repeat
unit. Is it Ok or do I need to specify all the atoms for all the repeat
units? Because when I run pdb2gmx it gives me warnging that several
atoms are missing. How do I enter chargegroup because in the .pdb file
chargegroup no. is different for different repeat unit. PLease tell me
about this. <br>
Thanking you in advance. looking forward to your kind reply.<br>
<br>
Rahul Karyappa<br>
NCL, Pune<br>
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