Re: [gmx-users] Topology file-residue unknown

On Sat, Apr 6, 2013 at 5:56 AM, Juliette N. wrote: > Thank you Justin. I have now the topology. I have a quick question > regarding atom types. I used opls_143 and opls_144 for C and H of ethylene > respec in rtp. However, in VMD I dont see double bonds C=C. I though maybe > these are not the pro

Re: [gmx-users] Topology file-residue unknown

Thank you Justin. I have now the topology. I have a quick question regarding atom types. I used opls_143 and opls_144 for C and H of ethylene respec in rtp. However, in VMD I dont see double bonds C=C. I though maybe these are not the proper atomtypes for H2C=CH2. rtp entry: [ atoms ] C1op

Re: [gmx-users] Topology file-residue unknown

On 4/4/13 6:17 PM, Juliette N. wrote: Hi Justin, Thanks a lot for your message. I am petrified why pdb2gmx is not recognizing the residue ETY. This the first residue added to ffoplsaa.rtp but as you may see below it is not read from rtp. I am sure this residue is added to ffoplsaa.rtp which i

Re: [gmx-users] Topology file-residue unknown

Hi Justin, Thanks a lot for your message. I am petrified why pdb2gmx is not recognizing the residue ETY. This the first residue added to ffoplsaa.rtp but as you may see below it is not read from rtp. I am sure this residue is added to ffoplsaa.rtp which is existing in the working directory: [ ET

Re: [gmx-users] Topology file-residue unknown

On 4/4/13 11:38 AM, Juliette N. wrote: Dear all, I am having trouble creating topology file for simple molecule ethylene. Here is the steps. Below is the pdb file: Ethylene.pdb: ATOM 1 C1 ETY 1 0.672 -0.000 0.000 1.00 0.00 C ATOM 2 C2 ETY 1 -0.672 -0.000

[gmx-users] Topology file-residue unknown

Dear all, I am having trouble creating topology file for simple molecule ethylene. Here is the steps. Below is the pdb file: Ethylene.pdb: ATOM 1 C1 ETY 1 0.672 -0.000 0.000 1.00 0.00 C ATOM 2 C2 ETY 1 -0.672 -0.000 0.000 1.00 0.00 C ATOM 3 H11 ETY