Alberto Arrigoni wrote:
*Dear gmx-users,
I am trying to insert a custom residue (a phosphoserine) in Gromacs
using force field Amber ff99sb-ildn.
I created a new .rtp entry named SEP like this:*
[SEP]
[ atoms ]
N N -0.49370 1
H H 0.30180 2
CA CT -0.23800 3
HA H1 0.09370 4
CB CT 0.07820 5
HB1 H1 -0.06020 6
HB2 H1 -0.06020 7
OG OS -0.55930 8
PS P 1.40000 9
OPA O2 -0.85000 10
OPB O2 -0.85000 11
OPC O2 -0.85000 12
C C 0.67310 13
O O -0.58540 14
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB OG
OG PS
PS OPA
PS OPB
PS OPC
C O
*After that, I got this error:*
WARNING: atom H is missing in residue SEP 124 in the pdb file
You might need to add atom H to the hydrogen database of
building block SEP
in the file aminoacids.hdb (see the manual)
WARNING: atom HA is missing in residue SEP 124 in the pdb file
You might need to add atom HA to the hydrogen database of
building block SEP
in the file aminoacids.hdb (see the manual)
WARNING: atom HB1 is missing in residue SEP 124 in the pdb file
You might need to add atom HB1 to the hydrogen database of
building block SEP
in the file aminoacids.hdb (see the manual)
WARNING: atom HB2 is missing in residue SEP 124 in the pdb file
You might need to add atom HB2 to the hydrogen database of
building block SEP
in the file aminoacids.hdb (see the manual)
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.3
Source code file: pdb2top.c, line: 1449
Fatal error:
There were 4 missing atoms in molecule Protein_chain_A, if you want to
use this incomplete topology anyhow, use the option -missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
*
So, I modified aminoacids.hdb adding a new entry for SEP:*
SEP 4
1 1 H N -C CA
1 5 HA CA N CB C
2 4 HB CB CA N
*
You have specified that there are 4 lines to be read for SEP (first line of the
entry), but only 3 follow it. This will raise the fatal error, because the file
format is now broken.
-Justin
but when I tried to use pdb2gmx in order to create .gro and .top files I
got the following error:*
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.3
Source code file: h_db.c, line: 174
Fatal error:
Error reading from file
/usr/local/gromacs/share/gromacs/top//amber99sb-ildn.ff/aminoacids.hdb
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
_______________________________
*This is not making any sense to me, since the file is still there, and
the only change was the new SEP entry...*
I appreciate any help you could give!
Best regards
Alberto
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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