AMBER Archive (2003)

Subject: problem with tleap

From: S.Swaminathan (swamy_at_www.cdfd.org.in)
Date: Tue Apr 08 2003 - 20:56:44 CDT

Hi

I am running leap (tleap) wherein I am loading the forcefield frcmod.pcy
and loading the protonated pdb file (BEST_WT.H.pdb). But when I give the
command 'saveamberparm' I am getting the following errors :

> saveamberparm sri prmtop.sri prmcrd.sri
Checking Unit.
WARNING: The unperturbed charge of the unit: 5.000000 is not zero.
FATAL: Atom .R<PRO 2>.A<HB1 15> does not have a type.
FATAL: Atom .R<PRO 2>.A<HG1 16> does not have a type.
FATAL: Atom .R<PRO 2>.A<HD1 17> does not have a type.
FATAL: Atom .R<PRO 3>.A<HB1 15> does not have a type.
FATAL: Atom .R<PRO 3>.A<HG1 16> does not have a type.
FATAL: Atom .R<PRO 3>.A<HD1 17> does not have a type.
FATAL: Atom .R<GLY 4>.A<HA1 8> does not have a type.
FATAL: Atom .R<PRO 5>.A<HB1 15> does not have a type.
FATAL: Atom .R<PRO 5>.A<HG1 16> does not have a type.
FATAL: Atom .R<PRO 5>.A<HD1 17> does not have a type.
FATAL: Atom .R<PHE 6>.A<HB1 21> does not have a type.

and also

FATAL: Atom .R<HEM 10479>.A<FE 1> does not have a type.
FATAL: Atom .R<HEM 10479>.A<CHA 2> does not have a type.
FATAL: Atom .R<HEM 10479>.A<HGM 3> does not have a type.
FATAL: Atom .R<HEM 10479>.A<CHB 4> does not have a type.
etc.

A.Why is this ? In case its because of libraries, how do i create
libraries for new residues for eg. HEM?
But the residues like PHE, GLY etc. are already existing, how do i load
them in tleap ?

B.the number indicated in case of :

FATAL: Atom .R<HEM 10479>.A<FE 1> does not have a type

is 10479, but in reality, there is no such residue number in the
atom file. Why is it so ? How do i rectify this ?

Swaminathan