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

[Oliver Grant]

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 <g0701207 at nus.edu.sg> wrote:

>  The termini were changed to NXXX/CXXX and the aminoacids.dat file has
> these two names as well. So nothing very evident.
>
> I can see that there was a thread on precisely this issue --- but how it
> was resolved is not very evident.
>
> http://www.mail-archive.com/gmx-users@gromacs.org/msg18545.html
>
>  ------------------------------
> *From:* gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On
> Behalf Of Jianguo Li [ljggmx at 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 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 <g0701207 at nus.edu.sg>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *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 error.
>
>  ------------------------------
> *From:* gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On
> Behalf Of Jianguo Li [ljggmx at yahoo.com.sg]
> *Sent:* Wednesday, August 24, 2011 3:06 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
>
>   you may need to use -ignh option in pdb2gmx.
> Jianguo
>
>  ------------------------------
> *From:* Kamesh Narasimhan <g0701207 at nus.edu.sg>
> *To:* "gmx-users at gromacs.org" <gmx-users at 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
>
>   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.rtp, and
> ffamber03.hdb the error could be -- if it's a nomenclature error. Would be
> great to receive some pointers on this.
>
> pdb2gmx -f prim_amb.pdb -o prim_amb.gro -water spc -ff amber03
> .
> .
> .
> .
> .
> WARNING: atom H is missing in residue GLY 1 in the pdb file
> You might need to add atom H to the hydrogen database of residue GLY
> in the file ff???.hdb (see the manual)
>
> ---------------------------------
>
> Program pdb2gmx, VERSION 4.0.5
>
> Source code file: pdb2top.C, line: 704
>
>
>
> Fatal error:
>
> There were 1 missing atoms in molecule Protein_C, if you want to use this
> incomplete topology anyhow, use the option-missing.
>
> I  get the error message complaining about a missing hydrogen in the first
> residue, no matter what that residue is --- say for instance even if I
> delete the first GLY residue from my pdb file.
>
> krish
>
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