RE: [gmx-users] error:You might need to add atom H to the hydrogen database of residue

?   From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Oliver Grant [olivercgr...@gmail.com] Sent: Wednesday, August 24, 2011 9:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue

Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue

rs-boun...@gromacs.org] On > Behalf Of Jianguo Li [ljg...@yahoo.com.sg] > *Sent:* Wednesday, August 24, 2011 3:46 PM > > *To:* Discussion list for GROMACS users > *Subject:* Re: [gmx-users] error:You might need to add atom H to the > hydrogen database of residue > > Not su

RE: [gmx-users] error:You might need to add atom H to the hydrogen database of residue

  From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Jianguo Li [ljg...@yahoo.com.sg] Sent: Wednesday, August 24, 2011 3:46 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue

Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue

Narasimhan To: Discussion list for GROMACS users Sent: Wednesday, 24 August 2011 15:10:13 Subject: RE: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Thanks Jianguo, It doesn't seem to make a difference even if i use -ignh -- I still get the same

RE: [gmx-users] error:You might need to add atom H to the hydrogen database of residue

t for GROMACS users Subject: Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue you may need to use -ignh option in pdb2gmx. Jianguo From: Kamesh Narasimhan To: "gmx-users@gromacs.org" Sent: Wednesday, 24 August 2011 14:42:28 Subject: [gmx-users]

Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue

you may need to use -ignh option in pdb2gmx. Jianguo From: Kamesh Narasimhan To: "gmx-users@gromacs.org" Sent: Wednesday, 24 August 2011 14:42:28 Subject: [gmx-users] error:You might need to add atom H to the hydrogen database of residue H

[gmx-users] error:You might need to add atom H to the hydrogen database of residue

Hi all,   I am using Gromacs 4.0.5 with the forcefield amber03 in a red hat linux machine to simulate a protein-DNA complex. Eventhough I manually edited my pdb file to adhere to the amber nomenclature, I get the below error.   I have not been able to pinpoint where in the pdb file, ffamber03