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 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-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 > > 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 <g0701...@nus.edu.sg> > *To:* Discussion list for GROMACS users <gmx-users@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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On > Behalf Of Jianguo Li [ljg...@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 <g0701...@nus.edu.sg> > *To:* "gmx-users@gromacs.org" <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 > > 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 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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