RE: [gmx-users] amber DNA non-integer charge

...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, August 29, 2011 3:06 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] amber DNA non-integer charge Kamesh Narasimhan wrote: > I am using Gromacs 4.0.5 and in my ffamber03.rtp I can see that the charges > are

RE: [gmx-users] amber DNA non-integer charge

_ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, August 29, 2011 2:41 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] amber DNA non-integer charge Kamesh Narasimha

RE: [gmx-users] amber DNA non-integer charge

Hil, I am trying to simulate a protein-DNA structure using amber03 and end up having a non-integer charge in topology generation . From the webpage of ffamber on NA-simulations, I could see this below instruction "However, for nucleic acids this also often causes pdb2gmx to replace an H atom

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

It's reading it as GLY tho so maybe you have NGLY in the wrong column? Maybe try move it over one to the right? Oliver On 24 August 2011 09:47, Kamesh Narasimhan <g0701...@nus.edu.sg> wrote: The termini were changed to NXXX/CXXX and the aminoacids.dat file has these two names

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

Not sure what is the problem. but if you have changed the name of the first/last residue as NXXX/CXXX, you may try to add these two names (NXXX and CXXX) to aminoacids.dat file (also change the number in the first line). Cheers, Jianguo From: Kamesh Narasimhan To: Discussion list for GROMACS

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]

[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